Starting phenix.real_space_refine on Fri Jul 3 23:02:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cc7_16557/07_2026/8cc7_16557.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cc7_16557/07_2026/8cc7_16557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8cc7_16557/07_2026/8cc7_16557.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cc7_16557/07_2026/8cc7_16557.cif" model { file = "/net/cci-nas-00/data/ceres_data/8cc7_16557/07_2026/8cc7_16557.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cc7_16557/07_2026/8cc7_16557.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cc7_16557/07_2026/8cc7_16557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cc7_16557/07_2026/8cc7_16557.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.052 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: 5 Type Number sf(0) Gaussians S 50 5.16 5 Cl 5 4.86 5 C 10960 2.51 5 N 2690 2.21 5 O 2945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 16650 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3231 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "B" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3231 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "C" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3231 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "D" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3231 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "E" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3231 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'NAG': 1, 'U9Q': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'NAG': 1, 'U9Q': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'NAG': 1, 'U9Q': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'NAG': 1, 'U9Q': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'NAG': 1, 'U9Q': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.75, per 1000 atoms: 0.23 Number of scatterers: 16650 At special positions: 0 Unit cell: (95.035, 96.18, 169.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 5 17.00 S 50 16.00 O 2945 8.00 N 2690 7.00 C 10960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 501 " - " ASN A 82 " " NAG B 501 " - " ASN B 82 " " NAG C 501 " - " ASN C 82 " " NAG D 501 " - " ASN D 82 " " NAG E 502 " - " ASN E 82 " " NAG F 1 " - " ASN A 164 " " NAG G 1 " - " ASN A 148 " " NAG H 1 " - " ASN B 164 " " NAG I 1 " - " ASN B 148 " " NAG J 1 " - " ASN C 164 " " NAG K 1 " - " ASN C 148 " " NAG L 1 " - " ASN D 164 " " NAG M 1 " - " ASN D 148 " " NAG N 1 " - " ASN E 164 " " NAG O 1 " - " ASN E 148 " Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 797.3 milliseconds 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3790 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 15 sheets defined 48.5% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 223 through 242 removed outlier: 3.789A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 243 through 244 No H-bonds generated for 'chain 'A' and resid 243 through 244' Processing helix chain 'A' and resid 245 through 249 removed outlier: 4.091A pdb=" N GLY A 249 " --> pdb=" O PRO A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 270 Processing helix chain 'A' and resid 282 through 309 removed outlier: 3.815A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 333 removed outlier: 3.790A pdb=" N ILE A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 460 removed outlier: 3.740A pdb=" N GLU A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 76 through 80 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 141 through 144 Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 223 through 242 removed outlier: 3.793A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 243 through 244 No H-bonds generated for 'chain 'B' and resid 243 through 244' Processing helix chain 'B' and resid 245 through 249 removed outlier: 4.097A pdb=" N GLY B 249 " --> pdb=" O PRO B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 270 Processing helix chain 'B' and resid 282 through 309 removed outlier: 3.786A pdb=" N TYR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 333 removed outlier: 3.799A pdb=" N ILE B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 460 removed outlier: 3.728A pdb=" N GLU B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 21 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 223 through 242 removed outlier: 3.797A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 243 through 244 No H-bonds generated for 'chain 'C' and resid 243 through 244' Processing helix chain 'C' and resid 245 through 249 removed outlier: 4.107A pdb=" N GLY C 249 " --> pdb=" O PRO C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 270 Processing helix chain 'C' and resid 282 through 309 removed outlier: 3.817A pdb=" N TYR C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 333 removed outlier: 3.820A pdb=" N ILE C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 460 removed outlier: 3.753A pdb=" N GLU C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 406 " --> pdb=" O LEU C 402 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 21 Processing helix chain 'D' and resid 76 through 80 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 141 through 144 Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 220 through 222 No H-bonds generated for 'chain 'D' and resid 220 through 222' Processing helix chain 'D' and resid 223 through 242 removed outlier: 3.803A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 243 through 244 No H-bonds generated for 'chain 'D' and resid 243 through 244' Processing helix chain 'D' and resid 245 through 249 removed outlier: 4.126A pdb=" N GLY D 249 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 270 Processing helix chain 'D' and resid 282 through 309 removed outlier: 3.811A pdb=" N TYR D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 removed outlier: 3.828A pdb=" N ILE D 329 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 460 removed outlier: 3.756A pdb=" N GLU D 405 " --> pdb=" O GLY D 401 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 21 Processing helix chain 'E' and resid 76 through 80 Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 141 through 144 Processing helix chain 'E' and resid 170 through 176 Processing helix chain 'E' and resid 220 through 222 No H-bonds generated for 'chain 'E' and resid 220 through 222' Processing helix chain 'E' and resid 223 through 242 removed outlier: 3.787A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 243 through 244 No H-bonds generated for 'chain 'E' and resid 243 through 244' Processing helix chain 'E' and resid 245 through 249 removed outlier: 4.109A pdb=" N GLY E 249 " --> pdb=" O PRO E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 270 Processing helix chain 'E' and resid 282 through 309 removed outlier: 3.803A pdb=" N TYR E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 333 removed outlier: 3.823A pdb=" N ILE E 329 " --> pdb=" O VAL E 325 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ALA E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 460 removed outlier: 3.743A pdb=" N GLU E 405 " --> pdb=" O GLY E 401 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.866A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL A 132 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.866A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N TRP A 63 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TYR A 46 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ARG A 65 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILE A 44 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N TYR A 67 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASP A 42 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N THR A 69 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 9.603A pdb=" N SER A 40 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.217A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.893A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL B 132 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.893A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N TRP B 63 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TYR B 46 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ARG B 65 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE B 44 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR B 67 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ASP B 42 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N THR B 69 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N SER B 40 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.204A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 85 through 89 removed outlier: 6.859A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL C 132 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 89 removed outlier: 6.859A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR C 61 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ILE C 48 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N TRP C 63 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR C 46 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ARG C 65 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE C 44 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N TYR C 67 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP C 42 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N THR C 69 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 9.589A pdb=" N SER C 40 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.232A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 85 through 89 removed outlier: 6.862A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL D 132 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 85 through 89 removed outlier: 6.862A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ARG D 65 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE D 44 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N TYR D 67 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ASP D 42 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N THR D 69 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N SER D 40 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.226A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.844A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL E 132 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.844A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ARG E 65 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE E 44 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TYR E 67 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ASP E 42 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N THR E 69 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N SER E 40 " --> pdb=" O THR E 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.230A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 939 hydrogen bonds defined for protein. 2742 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: 2.81 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5055 1.34 - 1.46: 4085 1.46 - 1.58: 7890 1.58 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 17115 Sorted by residual: bond pdb=" C23 U9Q E 501 " pdb=" N24 U9Q E 501 " ideal model delta sigma weight residual 1.384 1.486 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C23 U9Q C 502 " pdb=" N24 U9Q C 502 " ideal model delta sigma weight residual 1.384 1.485 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" C23 U9Q B 502 " pdb=" N24 U9Q B 502 " ideal model delta sigma weight residual 1.384 1.485 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" C23 U9Q A 502 " pdb=" N24 U9Q A 502 " ideal model delta sigma weight residual 1.384 1.485 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C23 U9Q D 502 " pdb=" N24 U9Q D 502 " ideal model delta sigma weight residual 1.384 1.485 -0.101 2.00e-02 2.50e+03 2.54e+01 ... (remaining 17110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 23013 2.26 - 4.51: 314 4.51 - 6.77: 62 6.77 - 9.02: 6 9.02 - 11.28: 5 Bond angle restraints: 23400 Sorted by residual: angle pdb=" C06 U9Q B 502 " pdb=" S08 U9Q B 502 " pdb=" N11 U9Q B 502 " ideal model delta sigma weight residual 103.05 114.33 -11.28 3.00e+00 1.11e-01 1.41e+01 angle pdb=" C06 U9Q C 502 " pdb=" S08 U9Q C 502 " pdb=" N11 U9Q C 502 " ideal model delta sigma weight residual 103.05 114.31 -11.26 3.00e+00 1.11e-01 1.41e+01 angle pdb=" C06 U9Q A 502 " pdb=" S08 U9Q A 502 " pdb=" N11 U9Q A 502 " ideal model delta sigma weight residual 103.05 113.99 -10.94 3.00e+00 1.11e-01 1.33e+01 angle pdb=" C06 U9Q D 502 " pdb=" S08 U9Q D 502 " pdb=" N11 U9Q D 502 " ideal model delta sigma weight residual 103.05 113.81 -10.76 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C06 U9Q E 501 " pdb=" S08 U9Q E 501 " pdb=" N11 U9Q E 501 " ideal model delta sigma weight residual 103.05 113.65 -10.60 3.00e+00 1.11e-01 1.25e+01 ... (remaining 23395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 8628 17.25 - 34.51: 980 34.51 - 51.76: 252 51.76 - 69.02: 20 69.02 - 86.27: 20 Dihedral angle restraints: 9900 sinusoidal: 4085 harmonic: 5815 Sorted by residual: dihedral pdb=" CG ARG C 315 " pdb=" CD ARG C 315 " pdb=" NE ARG C 315 " pdb=" CZ ARG C 315 " ideal model delta sinusoidal sigma weight residual 90.00 41.08 48.92 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CG ARG B 315 " pdb=" CD ARG B 315 " pdb=" NE ARG B 315 " pdb=" CZ ARG B 315 " ideal model delta sinusoidal sigma weight residual 90.00 41.10 48.90 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CG ARG D 315 " pdb=" CD ARG D 315 " pdb=" NE ARG D 315 " pdb=" CZ ARG D 315 " ideal model delta sinusoidal sigma weight residual 90.00 41.20 48.80 2 1.50e+01 4.44e-03 1.21e+01 ... (remaining 9897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1645 0.029 - 0.057: 656 0.057 - 0.086: 243 0.086 - 0.114: 165 0.114 - 0.143: 51 Chirality restraints: 2760 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 148 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN E 148 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN D 148 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 2757 not shown) Planarity restraints: 2835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 456 " 0.009 2.00e-02 2.50e+03 9.16e-03 2.10e+00 pdb=" CG TRP C 456 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP C 456 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP C 456 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 456 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 456 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 456 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 456 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 456 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 456 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 456 " 0.009 2.00e-02 2.50e+03 8.82e-03 1.95e+00 pdb=" CG TRP E 456 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP E 456 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP E 456 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 456 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 456 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 456 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 456 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 456 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 456 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 456 " 0.008 2.00e-02 2.50e+03 8.06e-03 1.62e+00 pdb=" CG TRP B 456 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP B 456 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 456 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 456 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 456 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 456 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 456 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 456 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 456 " 0.000 2.00e-02 2.50e+03 ... (remaining 2832 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2775 2.77 - 3.30: 15722 3.30 - 3.84: 28706 3.84 - 4.37: 31680 4.37 - 4.90: 57442 Nonbonded interactions: 136325 Sorted by model distance: nonbonded pdb=" OE2 GLU E 53 " pdb=" NH2 ARG E 218 " model vdw 2.239 3.120 nonbonded pdb=" OE2 GLU A 53 " pdb=" NH2 ARG A 218 " model vdw 2.243 3.120 nonbonded pdb=" OE2 GLU B 53 " pdb=" NH2 ARG B 218 " model vdw 2.248 3.120 nonbonded pdb=" O HIS A 309 " pdb=" NE2 GLN A 314 " model vdw 2.248 3.120 nonbonded pdb=" O HIS D 309 " pdb=" NE2 GLN D 314 " model vdw 2.249 3.120 ... (remaining 136320 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' and resid 8 through 460) selection = (chain 'B' and resid 8 through 460) selection = (chain 'C' and resid 8 through 460) selection = (chain 'D' and resid 8 through 460) selection = (chain 'E' and resid 8 through 460) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.690 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 0.004 0.102 17140 Z= 0.201 Angle : 0.652 11.279 23475 Z= 0.298 Chirality : 0.042 0.143 2760 Planarity : 0.004 0.037 2820 Dihedral : 15.559 86.271 6110 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.55 % Allowed : 19.40 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.20), residues: 1930 helix: 3.34 (0.17), residues: 780 sheet: -0.82 (0.23), residues: 440 loop : 0.57 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 315 TYR 0.015 0.001 TYR A 262 PHE 0.009 0.001 PHE B 181 TRP 0.025 0.001 TRP C 456 HIS 0.002 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 (17115) covalent geometry : angle 0.64733 / 0.30 (23400) hydrogen bonds : bond 0.14290 / 9.11 ( 904) hydrogen bonds : angle 6.12211 / 4.27 ( 2742) link_BETA1-4 : bond 0.00238 / 0.13 ( 10) link_BETA1-4 : angle 1.88923 / 1.14 ( 30) link_NAG-ASN : bond 0.00112 / 0.07 ( 15) link_NAG-ASN : angle 1.18001 / 0.86 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 0.785 Fit side-chains REVERT: A 52 ASP cc_start: 0.7808 (t0) cc_final: 0.6860 (t70) REVERT: A 54 LYS cc_start: 0.8114 (mtmm) cc_final: 0.7578 (mtmm) REVERT: A 105 ASP cc_start: 0.8073 (t0) cc_final: 0.7854 (t0) REVERT: B 41 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8286 (mp) REVERT: B 79 ASP cc_start: 0.8576 (m-30) cc_final: 0.8368 (m-30) REVERT: C 79 ASP cc_start: 0.8674 (m-30) cc_final: 0.8448 (m-30) REVERT: E 79 ASP cc_start: 0.8514 (m-30) cc_final: 0.8305 (m-30) outliers start: 10 outliers final: 7 residues processed: 177 average time/residue: 0.5346 time to fit residues: 106.9371 Evaluate side-chains 168 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 332 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 ASN D 119 HIS D 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101061 restraints weight = 20958.022| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.45 r_work: 0.2995 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17140 Z= 0.110 Angle : 0.516 5.576 23475 Z= 0.261 Chirality : 0.042 0.147 2760 Planarity : 0.004 0.034 2820 Dihedral : 5.703 42.156 2279 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.70 % Allowed : 16.92 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.20), residues: 1930 helix: 3.50 (0.17), residues: 775 sheet: -0.84 (0.23), residues: 445 loop : 0.52 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 315 TYR 0.013 0.001 TYR B 67 PHE 0.005 0.001 PHE A 233 TRP 0.016 0.001 TRP E 456 HIS 0.002 0.001 HIS B 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (17115) covalent geometry : angle 0.50825 / 0.26 (23400) hydrogen bonds : bond 0.04300 / 2.88 ( 904) hydrogen bonds : angle 4.59210 / 3.23 ( 2742) link_BETA1-4 : bond 0.00357 / 0.20 ( 10) link_BETA1-4 : angle 1.52422 / 0.99 ( 30) link_NAG-ASN : bond 0.00060 / 0.03 ( 15) link_NAG-ASN : angle 1.68892 / 1.19 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.682 Fit side-chains REVERT: A 52 ASP cc_start: 0.7331 (t0) cc_final: 0.6607 (t0) REVERT: A 105 ASP cc_start: 0.8056 (t0) cc_final: 0.7563 (t0) REVERT: B 41 ILE cc_start: 0.8661 (mt) cc_final: 0.8391 (mp) REVERT: B 434 ASP cc_start: 0.8367 (t0) cc_final: 0.8160 (t0) REVERT: C 41 ILE cc_start: 0.8811 (mt) cc_final: 0.8509 (mp) REVERT: C 50 ASN cc_start: 0.7829 (t0) cc_final: 0.7507 (t0) REVERT: C 328 ARG cc_start: 0.4587 (OUTLIER) cc_final: 0.4211 (mmm-85) REVERT: D 84 THR cc_start: 0.8451 (p) cc_final: 0.8243 (m) REVERT: D 99 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.8014 (pp) REVERT: D 120 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7930 (mtp85) REVERT: E 103 PHE cc_start: 0.8482 (m-80) cc_final: 0.8267 (m-10) REVERT: E 108 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7835 (mtmm) REVERT: E 328 ARG cc_start: 0.4471 (OUTLIER) cc_final: 0.4227 (mmm-85) outliers start: 31 outliers final: 11 residues processed: 182 average time/residue: 0.5296 time to fit residues: 109.0189 Evaluate side-chains 169 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 328 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 110 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 157 optimal weight: 3.9990 chunk 172 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.100377 restraints weight = 21042.803| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.43 r_work: 0.3024 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17140 Z= 0.109 Angle : 0.493 5.531 23475 Z= 0.249 Chirality : 0.042 0.141 2760 Planarity : 0.004 0.035 2820 Dihedral : 5.329 27.372 2269 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.47 % Allowed : 17.42 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.19), residues: 1930 helix: 3.52 (0.17), residues: 775 sheet: -0.79 (0.24), residues: 415 loop : 0.38 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 315 TYR 0.014 0.001 TYR B 67 PHE 0.005 0.001 PHE C 303 TRP 0.017 0.001 TRP E 456 HIS 0.002 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (17115) covalent geometry : angle 0.48531 / 0.25 (23400) hydrogen bonds : bond 0.04042 / 2.71 ( 904) hydrogen bonds : angle 4.37456 / 3.08 ( 2742) link_BETA1-4 : bond 0.00264 / 0.15 ( 10) link_BETA1-4 : angle 1.54667 / 0.99 ( 30) link_NAG-ASN : bond 0.00149 / 0.09 ( 15) link_NAG-ASN : angle 1.59761 / 1.10 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 0.608 Fit side-chains REVERT: A 52 ASP cc_start: 0.7511 (t0) cc_final: 0.6748 (t0) REVERT: A 54 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7650 (mtmm) REVERT: A 105 ASP cc_start: 0.8269 (t0) cc_final: 0.7831 (t0) REVERT: B 41 ILE cc_start: 0.8802 (mt) cc_final: 0.8594 (mp) REVERT: B 52 ASP cc_start: 0.7473 (t0) cc_final: 0.6795 (t0) REVERT: B 120 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7981 (mtp85) REVERT: B 250 GLU cc_start: 0.8096 (pt0) cc_final: 0.7800 (pm20) REVERT: B 315 ARG cc_start: 0.8352 (mtp85) cc_final: 0.8035 (mmm-85) REVERT: B 434 ASP cc_start: 0.8670 (t0) cc_final: 0.8444 (t0) REVERT: C 17 ASP cc_start: 0.7883 (t0) cc_final: 0.7231 (m-30) REVERT: C 41 ILE cc_start: 0.8868 (mt) cc_final: 0.8633 (mp) REVERT: C 201 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7681 (mm) REVERT: D 52 ASP cc_start: 0.7207 (t0) cc_final: 0.6743 (t0) REVERT: D 105 ASP cc_start: 0.8539 (t0) cc_final: 0.8320 (t0) REVERT: D 120 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8059 (mtp85) REVERT: D 331 TRP cc_start: 0.7529 (t60) cc_final: 0.7323 (t60) REVERT: E 103 PHE cc_start: 0.8585 (m-80) cc_final: 0.8359 (m-10) REVERT: E 108 LYS cc_start: 0.8336 (mtmm) cc_final: 0.7950 (mtmm) REVERT: E 201 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7482 (mm) REVERT: E 328 ARG cc_start: 0.4922 (OUTLIER) cc_final: 0.4362 (mmm-85) outliers start: 45 outliers final: 14 residues processed: 196 average time/residue: 0.5008 time to fit residues: 111.2378 Evaluate side-chains 179 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 328 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 95 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 149 optimal weight: 0.4980 chunk 143 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 162 optimal weight: 0.0070 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.128477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.102469 restraints weight = 20927.255| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.49 r_work: 0.3039 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17140 Z= 0.096 Angle : 0.485 7.473 23475 Z= 0.242 Chirality : 0.041 0.165 2760 Planarity : 0.004 0.040 2820 Dihedral : 4.977 24.697 2269 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.02 % Allowed : 16.98 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.20), residues: 1930 helix: 3.58 (0.17), residues: 775 sheet: -0.76 (0.25), residues: 415 loop : 0.39 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 315 TYR 0.013 0.001 TYR D 67 PHE 0.006 0.001 PHE A 233 TRP 0.017 0.001 TRP C 456 HIS 0.002 0.000 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.10 (17115) covalent geometry : angle 0.47786 / 0.24 (23400) hydrogen bonds : bond 0.03783 / 2.54 ( 904) hydrogen bonds : angle 4.18526 / 2.95 ( 2742) link_BETA1-4 : bond 0.00361 / 0.20 ( 10) link_BETA1-4 : angle 1.53936 / 0.99 ( 30) link_NAG-ASN : bond 0.00088 / 0.05 ( 15) link_NAG-ASN : angle 1.48558 / 1.02 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 0.610 Fit side-chains REVERT: A 52 ASP cc_start: 0.7507 (t0) cc_final: 0.6706 (t0) REVERT: A 54 LYS cc_start: 0.8224 (mtmm) cc_final: 0.7638 (mtmm) REVERT: A 105 ASP cc_start: 0.8179 (t0) cc_final: 0.7670 (t0) REVERT: A 184 GLN cc_start: 0.6930 (pt0) cc_final: 0.6037 (pm20) REVERT: B 52 ASP cc_start: 0.7378 (t0) cc_final: 0.6634 (t0) REVERT: B 105 ASP cc_start: 0.8428 (t0) cc_final: 0.7961 (t0) REVERT: B 120 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7888 (mtp85) REVERT: B 184 GLN cc_start: 0.6843 (OUTLIER) cc_final: 0.6003 (pm20) REVERT: B 315 ARG cc_start: 0.8299 (mtp85) cc_final: 0.7956 (mmm-85) REVERT: B 328 ARG cc_start: 0.4688 (OUTLIER) cc_final: 0.3980 (mtt-85) REVERT: B 434 ASP cc_start: 0.8583 (t0) cc_final: 0.8343 (t0) REVERT: C 52 ASP cc_start: 0.7603 (t0) cc_final: 0.6811 (t0) REVERT: C 201 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7700 (mm) REVERT: C 328 ARG cc_start: 0.5094 (OUTLIER) cc_final: 0.4328 (mmm-85) REVERT: D 52 ASP cc_start: 0.7244 (t0) cc_final: 0.6712 (t0) REVERT: D 120 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7846 (mtp85) REVERT: D 184 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6320 (pm20) REVERT: D 331 TRP cc_start: 0.7537 (t60) cc_final: 0.7335 (t60) REVERT: E 52 ASP cc_start: 0.7635 (t70) cc_final: 0.6946 (t0) REVERT: E 103 PHE cc_start: 0.8458 (m-80) cc_final: 0.8219 (m-10) REVERT: E 108 LYS cc_start: 0.8436 (mtmm) cc_final: 0.8052 (mtmm) REVERT: E 201 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7439 (mm) REVERT: E 311 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7081 (pp30) REVERT: E 328 ARG cc_start: 0.4923 (OUTLIER) cc_final: 0.4529 (mmm-85) outliers start: 55 outliers final: 18 residues processed: 195 average time/residue: 0.4914 time to fit residues: 108.7232 Evaluate side-chains 181 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 328 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 30 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 183 optimal weight: 0.0970 chunk 139 optimal weight: 2.9990 chunk 26 optimal weight: 0.0270 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.5036 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.128643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.102540 restraints weight = 20857.694| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.49 r_work: 0.3029 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17140 Z= 0.096 Angle : 0.483 6.422 23475 Z= 0.241 Chirality : 0.041 0.177 2760 Planarity : 0.004 0.039 2820 Dihedral : 4.832 23.278 2269 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.41 % Allowed : 16.32 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.20), residues: 1930 helix: 3.58 (0.17), residues: 775 sheet: -0.61 (0.25), residues: 405 loop : 0.39 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 315 TYR 0.013 0.001 TYR E 67 PHE 0.005 0.001 PHE B 254 TRP 0.018 0.001 TRP B 456 HIS 0.002 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (17115) covalent geometry : angle 0.47614 / 0.24 (23400) hydrogen bonds : bond 0.03695 / 2.48 ( 904) hydrogen bonds : angle 4.09098 / 2.88 ( 2742) link_BETA1-4 : bond 0.00299 / 0.17 ( 10) link_BETA1-4 : angle 1.53170 / 0.98 ( 30) link_NAG-ASN : bond 0.00114 / 0.07 ( 15) link_NAG-ASN : angle 1.48902 / 1.01 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 159 time to evaluate : 0.482 Fit side-chains REVERT: A 52 ASP cc_start: 0.7425 (t0) cc_final: 0.6581 (t0) REVERT: A 54 LYS cc_start: 0.8181 (mtmm) cc_final: 0.7547 (mtmm) REVERT: A 105 ASP cc_start: 0.8166 (t0) cc_final: 0.7645 (t0) REVERT: A 184 GLN cc_start: 0.6757 (OUTLIER) cc_final: 0.6057 (pm20) REVERT: A 328 ARG cc_start: 0.4839 (OUTLIER) cc_final: 0.4538 (mmm-85) REVERT: B 52 ASP cc_start: 0.7372 (t0) cc_final: 0.6636 (t0) REVERT: B 105 ASP cc_start: 0.8414 (t0) cc_final: 0.7937 (t0) REVERT: B 120 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7777 (mmm-85) REVERT: B 184 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.5997 (pm20) REVERT: B 250 GLU cc_start: 0.8061 (pm20) cc_final: 0.7627 (pm20) REVERT: B 315 ARG cc_start: 0.8285 (mtp85) cc_final: 0.7928 (mmm-85) REVERT: B 328 ARG cc_start: 0.4694 (OUTLIER) cc_final: 0.4002 (mtt-85) REVERT: B 434 ASP cc_start: 0.8589 (t0) cc_final: 0.8350 (t0) REVERT: C 52 ASP cc_start: 0.7491 (t0) cc_final: 0.6674 (t0) REVERT: C 201 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7679 (mm) REVERT: C 328 ARG cc_start: 0.5081 (OUTLIER) cc_final: 0.4356 (mmm-85) REVERT: D 17 ASP cc_start: 0.7903 (t0) cc_final: 0.7021 (m-30) REVERT: D 52 ASP cc_start: 0.7241 (t0) cc_final: 0.6666 (t0) REVERT: D 120 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7789 (mtp85) REVERT: D 184 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6353 (pm20) REVERT: E 17 ASP cc_start: 0.7813 (t0) cc_final: 0.6888 (m-30) REVERT: E 52 ASP cc_start: 0.7573 (t70) cc_final: 0.6894 (t0) REVERT: E 79 ASP cc_start: 0.8527 (m-30) cc_final: 0.8309 (m-30) REVERT: E 103 PHE cc_start: 0.8435 (m-80) cc_final: 0.8187 (m-10) REVERT: E 108 LYS cc_start: 0.8404 (mtmm) cc_final: 0.8003 (mtmm) REVERT: E 201 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7369 (mm) REVERT: E 328 ARG cc_start: 0.4989 (OUTLIER) cc_final: 0.4457 (mmm-85) outliers start: 62 outliers final: 19 residues processed: 209 average time/residue: 0.5010 time to fit residues: 118.9448 Evaluate side-chains 182 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 328 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 88 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 0.0370 chunk 26 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.127860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.101808 restraints weight = 20902.234| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.49 r_work: 0.3019 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17140 Z= 0.108 Angle : 0.491 6.216 23475 Z= 0.244 Chirality : 0.042 0.170 2760 Planarity : 0.004 0.038 2820 Dihedral : 4.766 22.303 2269 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.91 % Allowed : 16.65 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.20), residues: 1930 helix: 3.55 (0.17), residues: 775 sheet: -0.65 (0.25), residues: 400 loop : 0.34 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 315 TYR 0.014 0.001 TYR A 67 PHE 0.006 0.001 PHE C 233 TRP 0.021 0.001 TRP C 456 HIS 0.002 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (17115) covalent geometry : angle 0.48337 / 0.24 (23400) hydrogen bonds : bond 0.03704 / 2.49 ( 904) hydrogen bonds : angle 4.05059 / 2.86 ( 2742) link_BETA1-4 : bond 0.00267 / 0.15 ( 10) link_BETA1-4 : angle 1.55056 / 1.00 ( 30) link_NAG-ASN : bond 0.00150 / 0.09 ( 15) link_NAG-ASN : angle 1.57405 / 1.06 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 158 time to evaluate : 0.646 Fit side-chains REVERT: A 52 ASP cc_start: 0.7424 (t0) cc_final: 0.6545 (t0) REVERT: A 54 LYS cc_start: 0.8176 (mtmm) cc_final: 0.7516 (mtmm) REVERT: A 79 ASP cc_start: 0.8510 (m-30) cc_final: 0.8265 (m-30) REVERT: A 105 ASP cc_start: 0.8157 (t0) cc_final: 0.7627 (t0) REVERT: A 184 GLN cc_start: 0.6776 (OUTLIER) cc_final: 0.6064 (pm20) REVERT: A 328 ARG cc_start: 0.4849 (OUTLIER) cc_final: 0.4541 (mmm-85) REVERT: B 105 ASP cc_start: 0.8425 (t0) cc_final: 0.8007 (t0) REVERT: B 120 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7768 (mmm-85) REVERT: B 184 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.6001 (pm20) REVERT: B 250 GLU cc_start: 0.8206 (pm20) cc_final: 0.7729 (pm20) REVERT: B 315 ARG cc_start: 0.8297 (mtp85) cc_final: 0.7934 (mmm-85) REVERT: B 434 ASP cc_start: 0.8588 (t0) cc_final: 0.8336 (t0) REVERT: C 17 ASP cc_start: 0.7840 (t0) cc_final: 0.7222 (m-30) REVERT: C 52 ASP cc_start: 0.7481 (t0) cc_final: 0.6643 (t0) REVERT: C 201 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7630 (mm) REVERT: C 328 ARG cc_start: 0.4974 (OUTLIER) cc_final: 0.4283 (mmm-85) REVERT: D 17 ASP cc_start: 0.7902 (t0) cc_final: 0.6986 (m-30) REVERT: D 52 ASP cc_start: 0.7283 (t0) cc_final: 0.6748 (t0) REVERT: D 120 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7820 (mtp85) REVERT: D 184 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6331 (pm20) REVERT: E 17 ASP cc_start: 0.7860 (t0) cc_final: 0.7494 (OUTLIER) REVERT: E 52 ASP cc_start: 0.7428 (t70) cc_final: 0.6760 (t0) REVERT: E 103 PHE cc_start: 0.8470 (m-80) cc_final: 0.8223 (m-10) REVERT: E 108 LYS cc_start: 0.8412 (mtmm) cc_final: 0.8000 (mtmm) REVERT: E 201 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7297 (mm) REVERT: E 328 ARG cc_start: 0.4918 (OUTLIER) cc_final: 0.4330 (mmm-85) outliers start: 53 outliers final: 21 residues processed: 197 average time/residue: 0.4928 time to fit residues: 110.1604 Evaluate side-chains 183 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 328 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 155 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 118 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 113 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.101958 restraints weight = 20827.779| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.48 r_work: 0.3049 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17140 Z= 0.106 Angle : 0.496 6.821 23475 Z= 0.245 Chirality : 0.042 0.174 2760 Planarity : 0.004 0.041 2820 Dihedral : 4.651 21.184 2267 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.80 % Allowed : 16.76 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.20), residues: 1930 helix: 3.57 (0.17), residues: 775 sheet: -0.57 (0.25), residues: 405 loop : 0.31 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 315 TYR 0.014 0.001 TYR A 67 PHE 0.006 0.001 PHE E 233 TRP 0.019 0.001 TRP C 456 HIS 0.002 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (17115) covalent geometry : angle 0.48911 / 0.24 (23400) hydrogen bonds : bond 0.03669 / 2.47 ( 904) hydrogen bonds : angle 3.99792 / 2.82 ( 2742) link_BETA1-4 : bond 0.00272 / 0.15 ( 10) link_BETA1-4 : angle 1.53326 / 0.99 ( 30) link_NAG-ASN : bond 0.00153 / 0.09 ( 15) link_NAG-ASN : angle 1.53600 / 1.04 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 156 time to evaluate : 0.626 Fit side-chains REVERT: A 52 ASP cc_start: 0.7419 (t0) cc_final: 0.6523 (t0) REVERT: A 54 LYS cc_start: 0.8164 (mtmm) cc_final: 0.7488 (mtmm) REVERT: A 79 ASP cc_start: 0.8509 (m-30) cc_final: 0.8248 (m-30) REVERT: A 105 ASP cc_start: 0.8143 (t0) cc_final: 0.7708 (t0) REVERT: A 184 GLN cc_start: 0.6763 (OUTLIER) cc_final: 0.6084 (pm20) REVERT: A 328 ARG cc_start: 0.5048 (OUTLIER) cc_final: 0.4502 (mmm-85) REVERT: B 105 ASP cc_start: 0.8407 (t0) cc_final: 0.8000 (t0) REVERT: B 120 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7760 (mmm-85) REVERT: B 184 GLN cc_start: 0.6749 (OUTLIER) cc_final: 0.6010 (pm20) REVERT: B 250 GLU cc_start: 0.8194 (pm20) cc_final: 0.7723 (pm20) REVERT: B 315 ARG cc_start: 0.8432 (mtp85) cc_final: 0.8078 (mmm-85) REVERT: B 328 ARG cc_start: 0.4747 (OUTLIER) cc_final: 0.4048 (mtt180) REVERT: B 434 ASP cc_start: 0.8593 (t0) cc_final: 0.8334 (t0) REVERT: C 52 ASP cc_start: 0.7513 (t0) cc_final: 0.6668 (t0) REVERT: C 201 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7580 (mm) REVERT: C 328 ARG cc_start: 0.5042 (OUTLIER) cc_final: 0.4298 (mmm-85) REVERT: D 17 ASP cc_start: 0.7913 (t0) cc_final: 0.7007 (m-30) REVERT: D 52 ASP cc_start: 0.7299 (t0) cc_final: 0.6723 (t0) REVERT: D 120 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7812 (mtp85) REVERT: D 184 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6360 (pm20) REVERT: E 17 ASP cc_start: 0.7834 (t0) cc_final: 0.7614 (t0) REVERT: E 52 ASP cc_start: 0.7428 (t70) cc_final: 0.6662 (t0) REVERT: E 103 PHE cc_start: 0.8473 (m-80) cc_final: 0.8225 (m-10) REVERT: E 108 LYS cc_start: 0.8396 (mtmm) cc_final: 0.8109 (mtmm) REVERT: E 201 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7325 (mm) REVERT: E 328 ARG cc_start: 0.4962 (OUTLIER) cc_final: 0.4423 (mmm-85) outliers start: 51 outliers final: 25 residues processed: 194 average time/residue: 0.4592 time to fit residues: 101.2113 Evaluate side-chains 190 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 328 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 18 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.126661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.100620 restraints weight = 21009.225| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.48 r_work: 0.3007 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17140 Z= 0.127 Angle : 0.517 9.954 23475 Z= 0.254 Chirality : 0.042 0.163 2760 Planarity : 0.004 0.042 2820 Dihedral : 4.668 20.600 2267 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.75 % Allowed : 16.87 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.19), residues: 1930 helix: 3.51 (0.17), residues: 775 sheet: -0.67 (0.25), residues: 400 loop : 0.23 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 315 TYR 0.016 0.001 TYR C 67 PHE 0.006 0.001 PHE B 233 TRP 0.020 0.001 TRP E 331 HIS 0.003 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (17115) covalent geometry : angle 0.50969 / 0.25 (23400) hydrogen bonds : bond 0.03768 / 2.54 ( 904) hydrogen bonds : angle 3.98937 / 2.81 ( 2742) link_BETA1-4 : bond 0.00226 / 0.13 ( 10) link_BETA1-4 : angle 1.56509 / 1.02 ( 30) link_NAG-ASN : bond 0.00223 / 0.13 ( 15) link_NAG-ASN : angle 1.66040 / 1.12 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 0.679 Fit side-chains REVERT: A 17 ASP cc_start: 0.7788 (t0) cc_final: 0.6883 (m-30) REVERT: A 52 ASP cc_start: 0.7430 (t0) cc_final: 0.6570 (t0) REVERT: A 54 LYS cc_start: 0.8193 (mtmm) cc_final: 0.7613 (mtmm) REVERT: A 79 ASP cc_start: 0.8518 (m-30) cc_final: 0.8256 (m-30) REVERT: A 105 ASP cc_start: 0.8229 (t0) cc_final: 0.7676 (t0) REVERT: A 184 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6084 (pm20) REVERT: A 328 ARG cc_start: 0.5060 (OUTLIER) cc_final: 0.4501 (mmm-85) REVERT: B 52 ASP cc_start: 0.7658 (t0) cc_final: 0.6988 (t0) REVERT: B 105 ASP cc_start: 0.8413 (t0) cc_final: 0.8049 (t0) REVERT: B 116 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.8295 (m-80) REVERT: B 120 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7724 (mmm-85) REVERT: B 184 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6046 (pm20) REVERT: B 235 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6807 (mmp) REVERT: B 248 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.7923 (t) REVERT: B 250 GLU cc_start: 0.8221 (pm20) cc_final: 0.7231 (pm20) REVERT: B 315 ARG cc_start: 0.8520 (mtp85) cc_final: 0.8168 (mmm-85) REVERT: B 434 ASP cc_start: 0.8630 (t0) cc_final: 0.8347 (t0) REVERT: C 52 ASP cc_start: 0.7614 (t0) cc_final: 0.6774 (t0) REVERT: C 201 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7572 (mm) REVERT: C 328 ARG cc_start: 0.5051 (OUTLIER) cc_final: 0.4266 (mmm-85) REVERT: D 17 ASP cc_start: 0.7937 (t0) cc_final: 0.7003 (m-30) REVERT: D 52 ASP cc_start: 0.7276 (t0) cc_final: 0.6625 (t0) REVERT: D 120 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7871 (mtp85) REVERT: D 184 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6328 (pm20) REVERT: E 17 ASP cc_start: 0.7880 (t0) cc_final: 0.7632 (t0) REVERT: E 52 ASP cc_start: 0.7445 (t70) cc_final: 0.6812 (t70) REVERT: E 103 PHE cc_start: 0.8528 (m-80) cc_final: 0.8280 (m-10) REVERT: E 108 LYS cc_start: 0.8385 (mtmm) cc_final: 0.7998 (mtmm) REVERT: E 201 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7341 (mm) REVERT: E 328 ARG cc_start: 0.5018 (OUTLIER) cc_final: 0.4446 (mmm-85) outliers start: 50 outliers final: 25 residues processed: 195 average time/residue: 0.4705 time to fit residues: 104.4410 Evaluate side-chains 195 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 328 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 94 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.099870 restraints weight = 20976.981| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.47 r_work: 0.2993 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17140 Z= 0.143 Angle : 0.533 8.847 23475 Z= 0.262 Chirality : 0.043 0.161 2760 Planarity : 0.004 0.043 2820 Dihedral : 4.712 20.305 2267 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.53 % Allowed : 17.31 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.19), residues: 1930 helix: 3.47 (0.17), residues: 775 sheet: -0.86 (0.24), residues: 430 loop : 0.21 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 315 TYR 0.017 0.001 TYR A 67 PHE 0.009 0.001 PHE C 233 TRP 0.028 0.001 TRP E 456 HIS 0.002 0.001 HIS C 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (17115) covalent geometry : angle 0.52562 / 0.26 (23400) hydrogen bonds : bond 0.03869 / 2.61 ( 904) hydrogen bonds : angle 4.00541 / 2.81 ( 2742) link_BETA1-4 : bond 0.00209 / 0.12 ( 10) link_BETA1-4 : angle 1.58488 / 1.03 ( 30) link_NAG-ASN : bond 0.00266 / 0.16 ( 15) link_NAG-ASN : angle 1.74741 / 1.17 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.614 Fit side-chains REVERT: A 17 ASP cc_start: 0.7828 (t0) cc_final: 0.6918 (m-30) REVERT: A 52 ASP cc_start: 0.7434 (t0) cc_final: 0.6516 (t70) REVERT: A 54 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7669 (mtmt) REVERT: A 79 ASP cc_start: 0.8495 (m-30) cc_final: 0.8240 (m-30) REVERT: A 105 ASP cc_start: 0.8246 (t0) cc_final: 0.7763 (t0) REVERT: A 184 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6100 (pm20) REVERT: A 328 ARG cc_start: 0.5067 (OUTLIER) cc_final: 0.4523 (mmm-85) REVERT: B 52 ASP cc_start: 0.7553 (t0) cc_final: 0.6991 (t0) REVERT: B 105 ASP cc_start: 0.8435 (t0) cc_final: 0.8019 (t0) REVERT: B 116 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8311 (m-80) REVERT: B 120 ARG cc_start: 0.8426 (mpp80) cc_final: 0.7768 (mmm-85) REVERT: B 184 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6041 (pm20) REVERT: B 235 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6860 (mmp) REVERT: B 248 SER cc_start: 0.8756 (OUTLIER) cc_final: 0.8002 (t) REVERT: B 250 GLU cc_start: 0.8198 (pm20) cc_final: 0.7222 (pm20) REVERT: B 434 ASP cc_start: 0.8657 (t0) cc_final: 0.8422 (t0) REVERT: C 52 ASP cc_start: 0.7609 (t0) cc_final: 0.6834 (t0) REVERT: C 201 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7564 (mm) REVERT: C 235 MET cc_start: 0.7760 (mmt) cc_final: 0.7507 (mmp) REVERT: D 52 ASP cc_start: 0.7276 (t0) cc_final: 0.6696 (t0) REVERT: D 99 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8177 (pp) REVERT: D 120 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7917 (mtp85) REVERT: D 184 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6364 (pm20) REVERT: E 17 ASP cc_start: 0.7870 (t0) cc_final: 0.7610 (t0) REVERT: E 52 ASP cc_start: 0.7483 (t70) cc_final: 0.6851 (t70) REVERT: E 103 PHE cc_start: 0.8544 (m-80) cc_final: 0.8304 (m-10) REVERT: E 108 LYS cc_start: 0.8403 (mtmm) cc_final: 0.8095 (mtmm) REVERT: E 201 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7349 (mm) REVERT: E 221 LEU cc_start: 0.8842 (tp) cc_final: 0.8484 (mm) REVERT: E 250 GLU cc_start: 0.8177 (pm20) cc_final: 0.7744 (pm20) REVERT: E 328 ARG cc_start: 0.5013 (OUTLIER) cc_final: 0.4607 (mmm-85) outliers start: 46 outliers final: 24 residues processed: 190 average time/residue: 0.4876 time to fit residues: 105.2991 Evaluate side-chains 185 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 328 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 56 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.125849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099897 restraints weight = 20948.570| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.47 r_work: 0.2999 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17140 Z= 0.139 Angle : 0.537 7.631 23475 Z= 0.264 Chirality : 0.043 0.160 2760 Planarity : 0.004 0.043 2820 Dihedral : 4.712 21.250 2267 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.25 % Allowed : 17.97 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.19), residues: 1930 helix: 3.47 (0.17), residues: 775 sheet: -0.97 (0.23), residues: 465 loop : 0.17 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 315 TYR 0.016 0.001 TYR B 67 PHE 0.010 0.001 PHE A 233 TRP 0.030 0.001 TRP E 456 HIS 0.002 0.001 HIS C 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (17115) covalent geometry : angle 0.52947 / 0.26 (23400) hydrogen bonds : bond 0.03865 / 2.61 ( 904) hydrogen bonds : angle 4.00384 / 2.81 ( 2742) link_BETA1-4 : bond 0.00232 / 0.13 ( 10) link_BETA1-4 : angle 1.59671 / 1.04 ( 30) link_NAG-ASN : bond 0.00246 / 0.15 ( 15) link_NAG-ASN : angle 1.70664 / 1.14 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.610 Fit side-chains REVERT: A 17 ASP cc_start: 0.7946 (t0) cc_final: 0.7006 (m-30) REVERT: A 52 ASP cc_start: 0.7538 (t0) cc_final: 0.6693 (t0) REVERT: A 54 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7609 (mtmt) REVERT: A 105 ASP cc_start: 0.8406 (t0) cc_final: 0.7923 (t0) REVERT: A 184 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.6011 (pm20) REVERT: A 328 ARG cc_start: 0.5047 (OUTLIER) cc_final: 0.4469 (mmm-85) REVERT: A 421 GLU cc_start: 0.7015 (tt0) cc_final: 0.6774 (mm-30) REVERT: B 52 ASP cc_start: 0.7609 (t0) cc_final: 0.7115 (t0) REVERT: B 105 ASP cc_start: 0.8387 (t0) cc_final: 0.8004 (t0) REVERT: B 116 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.8438 (m-80) REVERT: B 120 ARG cc_start: 0.8528 (mpp80) cc_final: 0.7792 (mmm-85) REVERT: B 184 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6000 (pm20) REVERT: B 235 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6911 (mmp) REVERT: B 248 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.7997 (t) REVERT: B 250 GLU cc_start: 0.8278 (pm20) cc_final: 0.7297 (pm20) REVERT: B 434 ASP cc_start: 0.8756 (t0) cc_final: 0.8464 (t0) REVERT: C 52 ASP cc_start: 0.7570 (t0) cc_final: 0.6808 (t0) REVERT: C 201 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7605 (mm) REVERT: C 235 MET cc_start: 0.7829 (mmt) cc_final: 0.7614 (mmt) REVERT: D 17 ASP cc_start: 0.8018 (t0) cc_final: 0.7140 (m-30) REVERT: D 52 ASP cc_start: 0.7355 (t0) cc_final: 0.6800 (t0) REVERT: D 99 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8238 (pp) REVERT: D 120 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8050 (mtp85) REVERT: E 17 ASP cc_start: 0.8016 (t0) cc_final: 0.7793 (t0) REVERT: E 52 ASP cc_start: 0.7497 (t70) cc_final: 0.6890 (t70) REVERT: E 103 PHE cc_start: 0.8631 (m-80) cc_final: 0.8412 (m-10) REVERT: E 108 LYS cc_start: 0.8322 (mtmm) cc_final: 0.8008 (mtmm) REVERT: E 201 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7330 (mm) REVERT: E 221 LEU cc_start: 0.8849 (tp) cc_final: 0.8506 (mm) REVERT: E 250 GLU cc_start: 0.8199 (pm20) cc_final: 0.7787 (pm20) REVERT: E 328 ARG cc_start: 0.4961 (OUTLIER) cc_final: 0.4493 (mmm-85) outliers start: 41 outliers final: 23 residues processed: 179 average time/residue: 0.4897 time to fit residues: 99.5980 Evaluate side-chains 184 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 328 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 42 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 183 optimal weight: 0.0970 chunk 141 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 184 GLN E 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.126103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.100247 restraints weight = 20870.907| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.46 r_work: 0.3007 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17140 Z= 0.128 Angle : 0.542 12.354 23475 Z= 0.264 Chirality : 0.042 0.157 2760 Planarity : 0.004 0.043 2820 Dihedral : 4.673 20.223 2267 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.98 % Allowed : 18.19 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.19), residues: 1930 helix: 3.47 (0.17), residues: 780 sheet: -1.00 (0.23), residues: 465 loop : 0.15 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 315 TYR 0.015 0.001 TYR A 67 PHE 0.008 0.001 PHE E 242 TRP 0.029 0.001 TRP E 456 HIS 0.002 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (17115) covalent geometry : angle 0.53540 / 0.26 (23400) hydrogen bonds : bond 0.03818 / 2.57 ( 904) hydrogen bonds : angle 3.98268 / 2.79 ( 2742) link_BETA1-4 : bond 0.00234 / 0.13 ( 10) link_BETA1-4 : angle 1.58005 / 1.03 ( 30) link_NAG-ASN : bond 0.00220 / 0.13 ( 15) link_NAG-ASN : angle 1.66628 / 1.12 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4054.63 seconds wall clock time: 70 minutes 8.15 seconds (4208.15 seconds total)