Starting phenix.real_space_refine on Sun Aug 24 03:49:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cc7_16557/08_2025/8cc7_16557.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cc7_16557/08_2025/8cc7_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 { model { file = "/net/cci-nas-00/data/ceres_data/8cc7_16557/08_2025/8cc7_16557.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cc7_16557/08_2025/8cc7_16557.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cc7_16557/08_2025/8cc7_16557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cc7_16557/08_2025/8cc7_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-2.0-5787/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.21, per 1000 atoms: 0.25 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: 1.61 Conformation dependent library (CDL) restraints added in 665.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.49 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: 2.37 Time building geometry restraints manager: 2.06 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: 9143 17.25 - 34.51: 980 34.51 - 51.76: 252 51.76 - 69.02: 30 69.02 - 86.27: 20 Dihedral angle restraints: 10425 sinusoidal: 4610 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 10422 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: 0.01 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: 1.030 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.150 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 : 15.126 86.271 6635 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 aren 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 covalent geometry : bond 0.00403 (17115) covalent geometry : angle 0.64733 (23400) hydrogen bonds : bond 0.14290 ( 904) hydrogen bonds : angle 6.12211 ( 2742) link_BETA1-4 : bond 0.00238 ( 10) link_BETA1-4 : angle 1.88923 ( 30) link_NAG-ASN : bond 0.00112 ( 15) link_NAG-ASN : angle 1.18001 ( 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 : 0.591 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: 0.5240 time to fit residues: 104.2366 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 : 0.598 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3470 r_free = 0.3470 target = 0.126327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101195 restraints weight = 20973.003| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.44 r_work: 0.2997 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 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 = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.0754 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= 0.109 Angle : 0.516 5.622 23475 Z= 0.260 Chirality : 0.042 0.147 2760 Planarity : 0.004 0.038 2820 Dihedral : 6.202 55.755 2804 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.70 % Allowed : 16.87 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.20), residues: 1930 helix: 3.48 (0.17), residues: 775 sheet: -0.78 (0.24), residues: 415 loop : 0.39 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 315 TYR 0.013 0.001 TYR B 67 PHE 0.006 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 covalent geometry : bond 0.00227 (17115) covalent geometry : angle 0.50954 (23400) hydrogen bonds : bond 0.04232 ( 904) hydrogen bonds : angle 4.55210 ( 2742) link_BETA1-4 : bond 0.00422 ( 10) link_BETA1-4 : angle 1.53396 ( 30) link_NAG-ASN : bond 0.00041 ( 15) link_NAG-ASN : angle 1.57690 ( 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 196 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.678 Fit side-chains REVERT: A 52 ASP cc_start: 0.7319 (t0) cc_final: 0.6603 (t0) REVERT: A 105 ASP cc_start: 0.8052 (t0) cc_final: 0.7559 (t0) REVERT: B 41 ILE cc_start: 0.8664 (mt) cc_final: 0.8388 (mp) REVERT: B 434 ASP cc_start: 0.8369 (t0) cc_final: 0.8156 (t0) REVERT: C 41 ILE cc_start: 0.8827 (mt) cc_final: 0.8527 (mp) REVERT: C 50 ASN cc_start: 0.7832 (t0) cc_final: 0.7522 (t0) REVERT: C 328 ARG cc_start: 0.4612 (OUTLIER) cc_final: 0.4237 (mmm-85) REVERT: D 84 THR cc_start: 0.8451 (p) cc_final: 0.8244 (m) REVERT: D 120 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7925 (mtp85) REVERT: E 52 ASP cc_start: 0.7208 (t70) cc_final: 0.6625 (t70) REVERT: E 103 PHE cc_start: 0.8463 (m-80) cc_final: 0.8245 (m-10) REVERT: E 108 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7840 (mtmm) REVERT: E 328 ARG cc_start: 0.4472 (OUTLIER) cc_final: 0.4228 (mmm-85) outliers start: 31 outliers final: 12 residues processed: 180 average time/residue: 0.5272 time to fit residues: 106.4835 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 : 0.581 ------------------------------------------------------------------------------- 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 B residue 332 ILE 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 120 ARG Chi-restraints excluded: chain D residue 332 ILE 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: 0.8980 chunk 69 optimal weight: 3.9990 chunk 105 optimal weight: 0.0070 chunk 140 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 172 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 119 optimal weight: 0.0470 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.128089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.101922 restraints weight = 21065.899| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.50 r_work: 0.3023 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 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 = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17140 Z= 0.098 Angle : 0.480 5.860 23475 Z= 0.243 Chirality : 0.041 0.140 2760 Planarity : 0.004 0.035 2820 Dihedral : 5.652 51.558 2794 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.42 % Allowed : 17.09 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.20), residues: 1930 helix: 3.54 (0.17), residues: 775 sheet: -0.79 (0.24), residues: 415 loop : 0.40 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 315 TYR 0.013 0.001 TYR D 67 PHE 0.005 0.001 PHE A 233 TRP 0.016 0.001 TRP E 456 HIS 0.002 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00201 (17115) covalent geometry : angle 0.47342 (23400) hydrogen bonds : bond 0.03932 ( 904) hydrogen bonds : angle 4.31570 ( 2742) link_BETA1-4 : bond 0.00302 ( 10) link_BETA1-4 : angle 1.67086 ( 30) link_NAG-ASN : bond 0.00080 ( 15) link_NAG-ASN : angle 1.38052 ( 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 206 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 0.509 Fit side-chains REVERT: A 52 ASP cc_start: 0.7448 (t0) cc_final: 0.6703 (t0) REVERT: A 54 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7665 (mtmm) REVERT: A 105 ASP cc_start: 0.8195 (t0) cc_final: 0.7754 (t0) REVERT: B 41 ILE cc_start: 0.8726 (mt) cc_final: 0.8525 (mp) REVERT: B 52 ASP cc_start: 0.7572 (t0) cc_final: 0.6876 (t0) REVERT: B 120 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7888 (mtp85) REVERT: B 184 GLN cc_start: 0.6935 (pt0) cc_final: 0.6037 (pm20) REVERT: B 315 ARG cc_start: 0.8249 (mtp85) cc_final: 0.7932 (mmm-85) REVERT: B 434 ASP cc_start: 0.8601 (t0) cc_final: 0.8389 (t0) REVERT: C 17 ASP cc_start: 0.7833 (t0) cc_final: 0.7249 (m-30) REVERT: C 201 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7803 (mm) REVERT: D 17 ASP cc_start: 0.7242 (m-30) cc_final: 0.7031 (m-30) REVERT: D 52 ASP cc_start: 0.7262 (t0) cc_final: 0.6788 (t0) REVERT: D 99 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8286 (pp) REVERT: D 120 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7939 (mtp85) REVERT: D 315 ARG cc_start: 0.8355 (mtp85) cc_final: 0.8137 (mmm160) REVERT: D 331 TRP cc_start: 0.7560 (t60) cc_final: 0.7351 (t60) REVERT: E 52 ASP cc_start: 0.7464 (t70) cc_final: 0.6881 (t70) REVERT: E 103 PHE cc_start: 0.8478 (m-80) cc_final: 0.8246 (m-10) REVERT: E 108 LYS cc_start: 0.8408 (mtmm) cc_final: 0.8043 (mtmm) REVERT: E 201 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7492 (mm) REVERT: E 328 ARG cc_start: 0.4982 (OUTLIER) cc_final: 0.4418 (mmm-85) outliers start: 44 outliers final: 12 residues processed: 193 average time/residue: 0.5520 time to fit residues: 120.1802 Evaluate side-chains 174 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 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 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 41 ILE 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 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: 0.5980 chunk 0 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 192 optimal weight: 0.7980 chunk 184 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 162 optimal weight: 0.4980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.097880 restraints weight = 21227.340| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.48 r_work: 0.2965 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 17140 Z= 0.190 Angle : 0.553 6.751 23475 Z= 0.276 Chirality : 0.044 0.155 2760 Planarity : 0.004 0.042 2820 Dihedral : 5.900 57.627 2794 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.96 % Allowed : 16.70 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.19), residues: 1930 helix: 3.32 (0.17), residues: 775 sheet: -0.90 (0.23), residues: 435 loop : 0.34 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 315 TYR 0.020 0.001 TYR C 67 PHE 0.009 0.001 PHE C 303 TRP 0.018 0.001 TRP C 456 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00461 (17115) covalent geometry : angle 0.54407 (23400) hydrogen bonds : bond 0.04342 ( 904) hydrogen bonds : angle 4.34029 ( 2742) link_BETA1-4 : bond 0.00205 ( 10) link_BETA1-4 : angle 1.76405 ( 30) link_NAG-ASN : bond 0.00342 ( 15) link_NAG-ASN : angle 1.84855 ( 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 230 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 158 time to evaluate : 0.691 Fit side-chains REVERT: A 52 ASP cc_start: 0.7603 (t0) cc_final: 0.6693 (t70) REVERT: A 54 LYS cc_start: 0.8216 (mtmm) cc_final: 0.7582 (mtmm) REVERT: A 105 ASP cc_start: 0.8328 (t0) cc_final: 0.7852 (t0) REVERT: A 184 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6096 (pm20) REVERT: B 52 ASP cc_start: 0.7483 (t0) cc_final: 0.6893 (t0) REVERT: B 105 ASP cc_start: 0.8654 (t0) cc_final: 0.8224 (t0) REVERT: B 120 ARG cc_start: 0.8548 (mpp80) cc_final: 0.7799 (mmm-85) REVERT: B 184 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6151 (pm20) REVERT: B 250 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7905 (pm20) REVERT: C 52 ASP cc_start: 0.7653 (t0) cc_final: 0.7000 (t0) REVERT: D 52 ASP cc_start: 0.7364 (t0) cc_final: 0.6891 (t0) REVERT: D 120 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8104 (mtp85) REVERT: E 17 ASP cc_start: 0.7975 (t0) cc_final: 0.7731 (OUTLIER) REVERT: E 52 ASP cc_start: 0.7548 (t70) cc_final: 0.6995 (t70) REVERT: E 103 PHE cc_start: 0.8626 (m-80) cc_final: 0.8422 (m-10) REVERT: E 108 LYS cc_start: 0.8477 (mtmm) cc_final: 0.8116 (mtmm) REVERT: E 201 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7520 (mm) REVERT: E 311 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7150 (pp30) outliers start: 72 outliers final: 28 residues processed: 210 average time/residue: 0.5043 time to fit residues: 120.4753 Evaluate side-chains 186 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE 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 332 ILE Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 268 ILE 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 120 ARG Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 227 LEU 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 311 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 30 optimal weight: 0.0570 chunk 168 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 26 optimal weight: 0.0010 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 overall best weight: 0.5706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.100774 restraints weight = 20901.544| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.47 r_work: 0.3012 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 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 = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1250 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= 0.102 Angle : 0.500 6.352 23475 Z= 0.250 Chirality : 0.042 0.148 2760 Planarity : 0.004 0.040 2820 Dihedral : 5.394 54.622 2792 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.58 % Allowed : 17.69 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.19), residues: 1930 helix: 3.51 (0.17), residues: 775 sheet: -0.94 (0.24), residues: 410 loop : 0.24 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 315 TYR 0.014 0.001 TYR E 67 PHE 0.005 0.001 PHE C 254 TRP 0.019 0.001 TRP E 456 HIS 0.002 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00217 (17115) covalent geometry : angle 0.49240 (23400) hydrogen bonds : bond 0.03889 ( 904) hydrogen bonds : angle 4.18793 ( 2742) link_BETA1-4 : bond 0.00368 ( 10) link_BETA1-4 : angle 1.73140 ( 30) link_NAG-ASN : bond 0.00109 ( 15) link_NAG-ASN : angle 1.46638 ( 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 207 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.648 Fit side-chains REVERT: A 52 ASP cc_start: 0.7477 (t0) cc_final: 0.6614 (t0) REVERT: A 54 LYS cc_start: 0.8186 (mtmm) cc_final: 0.7565 (mtmm) REVERT: A 105 ASP cc_start: 0.8186 (t0) cc_final: 0.7728 (t0) REVERT: A 184 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6030 (pm20) REVERT: B 52 ASP cc_start: 0.7409 (t0) cc_final: 0.6601 (t0) REVERT: B 105 ASP cc_start: 0.8452 (t0) cc_final: 0.7994 (t0) REVERT: B 120 ARG cc_start: 0.8391 (mpp80) cc_final: 0.7758 (mmm-85) REVERT: B 184 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6002 (pm20) REVERT: B 250 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: B 434 ASP cc_start: 0.8618 (t0) cc_final: 0.8375 (t0) REVERT: C 52 ASP cc_start: 0.7515 (t0) cc_final: 0.6730 (t0) REVERT: C 328 ARG cc_start: 0.5083 (OUTLIER) cc_final: 0.4325 (mmm-85) REVERT: C 434 ASP cc_start: 0.8513 (t0) cc_final: 0.8255 (t0) REVERT: D 17 ASP cc_start: 0.7922 (t0) cc_final: 0.6974 (m-30) REVERT: D 52 ASP cc_start: 0.7264 (t0) cc_final: 0.6761 (t0) REVERT: D 99 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8285 (pp) REVERT: D 120 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7964 (mtp85) REVERT: E 17 ASP cc_start: 0.7819 (t0) cc_final: 0.7505 (OUTLIER) REVERT: E 52 ASP cc_start: 0.7448 (t70) cc_final: 0.6862 (t70) REVERT: E 103 PHE cc_start: 0.8545 (m-80) cc_final: 0.8319 (m-10) REVERT: E 108 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8113 (mtmm) REVERT: E 201 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7428 (mm) REVERT: E 221 LEU cc_start: 0.8864 (tp) cc_final: 0.8487 (mm) REVERT: E 328 ARG cc_start: 0.5034 (OUTLIER) cc_final: 0.4542 (mmm-85) outliers start: 47 outliers final: 15 residues processed: 194 average time/residue: 0.5411 time to fit residues: 118.6928 Evaluate side-chains 174 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 332 ILE Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 259 LEU 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 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 201 ILE Chi-restraints excluded: chain E residue 296 ILE 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: 0.0770 chunk 147 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 80 optimal weight: 0.0370 chunk 180 optimal weight: 2.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.101481 restraints weight = 20879.140| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.48 r_work: 0.2992 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 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 = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17140 Z= 0.100 Angle : 0.491 6.373 23475 Z= 0.246 Chirality : 0.042 0.167 2760 Planarity : 0.004 0.037 2820 Dihedral : 5.029 49.403 2792 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.91 % Allowed : 16.54 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.19), residues: 1930 helix: 3.52 (0.17), residues: 775 sheet: -0.82 (0.24), residues: 415 loop : 0.27 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 315 TYR 0.013 0.001 TYR D 67 PHE 0.005 0.001 PHE C 233 TRP 0.021 0.001 TRP E 456 HIS 0.002 0.000 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00213 (17115) covalent geometry : angle 0.48409 (23400) hydrogen bonds : bond 0.03771 ( 904) hydrogen bonds : angle 4.08646 ( 2742) link_BETA1-4 : bond 0.00312 ( 10) link_BETA1-4 : angle 1.71338 ( 30) link_NAG-ASN : bond 0.00137 ( 15) link_NAG-ASN : angle 1.41660 ( 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 213 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 160 time to evaluate : 0.679 Fit side-chains REVERT: A 52 ASP cc_start: 0.7506 (t0) cc_final: 0.6705 (t0) REVERT: A 54 LYS cc_start: 0.8177 (mtmm) cc_final: 0.7454 (mtmm) REVERT: A 79 ASP cc_start: 0.8528 (m-30) cc_final: 0.8279 (m-30) REVERT: A 105 ASP cc_start: 0.8174 (t0) cc_final: 0.7725 (t0) REVERT: A 184 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6017 (pm20) REVERT: A 328 ARG cc_start: 0.4844 (OUTLIER) cc_final: 0.4538 (mmm-85) REVERT: B 52 ASP cc_start: 0.7404 (t0) cc_final: 0.6747 (t0) REVERT: B 105 ASP cc_start: 0.8429 (t0) cc_final: 0.7980 (t0) REVERT: B 120 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7735 (mmm-85) REVERT: B 184 GLN cc_start: 0.6849 (OUTLIER) cc_final: 0.6039 (pm20) REVERT: B 328 ARG cc_start: 0.4803 (OUTLIER) cc_final: 0.4124 (mtt180) REVERT: B 434 ASP cc_start: 0.8589 (t0) cc_final: 0.8333 (t0) REVERT: C 52 ASP cc_start: 0.7467 (t0) cc_final: 0.6658 (t0) REVERT: C 328 ARG cc_start: 0.4990 (OUTLIER) cc_final: 0.4319 (mmm-85) REVERT: C 434 ASP cc_start: 0.8422 (t0) cc_final: 0.8143 (t0) REVERT: D 17 ASP cc_start: 0.7865 (t0) cc_final: 0.6976 (m-30) REVERT: D 52 ASP cc_start: 0.7309 (t0) cc_final: 0.6739 (t0) REVERT: D 99 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8233 (pp) REVERT: D 120 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7901 (mtp85) REVERT: E 17 ASP cc_start: 0.7819 (t0) cc_final: 0.7491 (OUTLIER) REVERT: E 52 ASP cc_start: 0.7443 (t70) cc_final: 0.6856 (t70) REVERT: E 103 PHE cc_start: 0.8499 (m-80) cc_final: 0.8263 (m-10) REVERT: E 108 LYS cc_start: 0.8374 (mtmm) cc_final: 0.8045 (mtmm) REVERT: E 201 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7306 (mm) REVERT: E 221 LEU cc_start: 0.8880 (tp) cc_final: 0.8528 (mm) REVERT: E 328 ARG cc_start: 0.4885 (OUTLIER) cc_final: 0.4328 (mmm-85) outliers start: 53 outliers final: 21 residues processed: 195 average time/residue: 0.5657 time to fit residues: 124.2959 Evaluate side-chains 188 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 221 LEU Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 103 PHE 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 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 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 201 ILE Chi-restraints excluded: chain E residue 227 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: 0.9990 chunk 98 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.124649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.098806 restraints weight = 20979.688| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.46 r_work: 0.2988 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17140 Z= 0.159 Angle : 0.536 7.109 23475 Z= 0.266 Chirality : 0.043 0.177 2760 Planarity : 0.004 0.042 2820 Dihedral : 5.094 49.148 2792 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.80 % Allowed : 16.92 % 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 aren not related in a simple way. whole: 1.75 (0.19), residues: 1930 helix: 3.36 (0.17), residues: 775 sheet: -1.04 (0.23), residues: 440 loop : 0.21 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 315 TYR 0.022 0.001 TYR B 67 PHE 0.008 0.001 PHE C 233 TRP 0.023 0.001 TRP E 456 HIS 0.003 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00378 (17115) covalent geometry : angle 0.52723 (23400) hydrogen bonds : bond 0.04042 ( 904) hydrogen bonds : angle 4.16140 ( 2742) link_BETA1-4 : bond 0.00230 ( 10) link_BETA1-4 : angle 1.80069 ( 30) link_NAG-ASN : bond 0.00310 ( 15) link_NAG-ASN : angle 1.72946 ( 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 205 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 154 time to evaluate : 0.526 Fit side-chains REVERT: A 17 ASP cc_start: 0.7959 (t0) cc_final: 0.7042 (m-30) REVERT: A 52 ASP cc_start: 0.7606 (t0) cc_final: 0.6714 (t70) REVERT: A 54 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7671 (mtmt) REVERT: A 79 ASP cc_start: 0.8581 (m-30) cc_final: 0.8359 (m-30) REVERT: A 105 ASP cc_start: 0.8363 (t0) cc_final: 0.7901 (t0) REVERT: A 184 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6076 (pm20) REVERT: B 52 ASP cc_start: 0.7468 (t0) cc_final: 0.6815 (t0) REVERT: B 105 ASP cc_start: 0.8606 (t0) cc_final: 0.8217 (t0) REVERT: B 116 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.8440 (m-80) REVERT: B 120 ARG cc_start: 0.8554 (mpp80) cc_final: 0.7801 (mmm-85) REVERT: B 184 GLN cc_start: 0.7106 (OUTLIER) cc_final: 0.6147 (pm20) REVERT: B 235 MET cc_start: 0.7249 (tpp) cc_final: 0.7009 (mmm) REVERT: B 242 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8588 (t80) REVERT: C 52 ASP cc_start: 0.7575 (t0) cc_final: 0.6805 (t0) REVERT: D 17 ASP cc_start: 0.8063 (t0) cc_final: 0.7164 (m-30) REVERT: D 52 ASP cc_start: 0.7423 (t0) cc_final: 0.6802 (t0) REVERT: D 99 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8373 (pp) REVERT: D 120 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8119 (mtp85) REVERT: E 52 ASP cc_start: 0.7539 (t70) cc_final: 0.7023 (t70) REVERT: E 103 PHE cc_start: 0.8650 (m-80) cc_final: 0.8449 (m-10) REVERT: E 108 LYS cc_start: 0.8349 (mtmm) cc_final: 0.7985 (mtmm) REVERT: E 201 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7325 (mm) REVERT: E 221 LEU cc_start: 0.8911 (tp) cc_final: 0.8567 (mm) REVERT: E 328 ARG cc_start: 0.4938 (OUTLIER) cc_final: 0.4351 (mmm-85) outliers start: 51 outliers final: 23 residues processed: 195 average time/residue: 0.5217 time to fit residues: 115.1330 Evaluate side-chains 186 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 221 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 103 PHE 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 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 227 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.124903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.098921 restraints weight = 21024.099| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.46 r_work: 0.2992 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 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 = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17140 Z= 0.140 Angle : 0.529 7.985 23475 Z= 0.263 Chirality : 0.043 0.174 2760 Planarity : 0.004 0.043 2820 Dihedral : 4.967 46.882 2792 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.58 % Allowed : 17.36 % 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 aren not related in a simple way. whole: 1.75 (0.19), residues: 1930 helix: 3.42 (0.17), residues: 775 sheet: -1.07 (0.23), residues: 440 loop : 0.18 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 315 TYR 0.019 0.001 TYR B 67 PHE 0.006 0.001 PHE E 233 TRP 0.025 0.001 TRP E 456 HIS 0.002 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00327 (17115) covalent geometry : angle 0.52115 (23400) hydrogen bonds : bond 0.03963 ( 904) hydrogen bonds : angle 4.12836 ( 2742) link_BETA1-4 : bond 0.00261 ( 10) link_BETA1-4 : angle 1.79641 ( 30) link_NAG-ASN : bond 0.00224 ( 15) link_NAG-ASN : angle 1.63365 ( 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 203 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 0.721 Fit side-chains REVERT: A 17 ASP cc_start: 0.7903 (t0) cc_final: 0.7029 (m-30) REVERT: A 52 ASP cc_start: 0.7546 (t0) cc_final: 0.6650 (t70) REVERT: A 54 LYS cc_start: 0.8159 (mtmm) cc_final: 0.7643 (mtmt) REVERT: A 105 ASP cc_start: 0.8350 (t0) cc_final: 0.7887 (t0) REVERT: A 184 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.5977 (pm20) REVERT: B 52 ASP cc_start: 0.7466 (t0) cc_final: 0.6785 (t0) REVERT: B 105 ASP cc_start: 0.8619 (t0) cc_final: 0.8250 (t0) REVERT: B 116 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8441 (m-80) REVERT: B 120 ARG cc_start: 0.8553 (mpp80) cc_final: 0.7800 (mmm-85) REVERT: B 184 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6043 (pm20) REVERT: B 235 MET cc_start: 0.7193 (tpp) cc_final: 0.6958 (mmm) REVERT: B 242 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8627 (t80) REVERT: B 250 GLU cc_start: 0.8337 (pm20) cc_final: 0.7845 (pm20) REVERT: B 434 ASP cc_start: 0.8757 (t0) cc_final: 0.8538 (t0) REVERT: C 52 ASP cc_start: 0.7633 (t0) cc_final: 0.6820 (t0) REVERT: C 434 ASP cc_start: 0.8639 (t0) cc_final: 0.8381 (t0) REVERT: D 17 ASP cc_start: 0.8030 (t0) cc_final: 0.7130 (m-30) REVERT: D 52 ASP cc_start: 0.7374 (t0) cc_final: 0.6828 (t0) REVERT: D 99 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8345 (pp) REVERT: D 120 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8107 (mtp85) REVERT: E 52 ASP cc_start: 0.7489 (t70) cc_final: 0.6920 (t70) REVERT: E 103 PHE cc_start: 0.8637 (m-80) cc_final: 0.8431 (m-10) REVERT: E 108 LYS cc_start: 0.8337 (mtmm) cc_final: 0.7969 (mtmm) REVERT: E 201 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7280 (mm) REVERT: E 221 LEU cc_start: 0.8906 (tp) cc_final: 0.8560 (mm) REVERT: E 328 ARG cc_start: 0.4932 (OUTLIER) cc_final: 0.4376 (mmm-85) REVERT: E 434 ASP cc_start: 0.8619 (t0) cc_final: 0.8374 (t0) outliers start: 47 outliers final: 26 residues processed: 192 average time/residue: 0.5282 time to fit residues: 115.4697 Evaluate side-chains 187 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR 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 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 221 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 103 PHE 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 221 LEU Chi-restraints excluded: chain D residue 263 SER 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 227 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: 0.9980 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.098192 restraints weight = 21049.872| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.45 r_work: 0.2979 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17140 Z= 0.160 Angle : 0.545 6.947 23475 Z= 0.270 Chirality : 0.043 0.173 2760 Planarity : 0.004 0.043 2820 Dihedral : 4.975 44.476 2792 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.31 % Allowed : 17.47 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.19), residues: 1930 helix: 3.34 (0.17), residues: 775 sheet: -1.10 (0.23), residues: 440 loop : 0.11 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 315 TYR 0.020 0.001 TYR B 67 PHE 0.007 0.001 PHE C 233 TRP 0.027 0.001 TRP E 456 HIS 0.003 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00382 (17115) covalent geometry : angle 0.53704 (23400) hydrogen bonds : bond 0.04064 ( 904) hydrogen bonds : angle 4.14531 ( 2742) link_BETA1-4 : bond 0.00256 ( 10) link_BETA1-4 : angle 1.83426 ( 30) link_NAG-ASN : bond 0.00313 ( 15) link_NAG-ASN : angle 1.72867 ( 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 190 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.656 Fit side-chains REVERT: A 17 ASP cc_start: 0.7927 (t0) cc_final: 0.7042 (m-30) REVERT: A 52 ASP cc_start: 0.7574 (t0) cc_final: 0.6672 (t70) REVERT: A 54 LYS cc_start: 0.8153 (mtmm) cc_final: 0.7647 (mtmt) REVERT: A 79 ASP cc_start: 0.8572 (m-30) cc_final: 0.8342 (m-30) REVERT: A 105 ASP cc_start: 0.8352 (t0) cc_final: 0.7883 (t0) REVERT: A 184 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6122 (pm20) REVERT: B 52 ASP cc_start: 0.7480 (t0) cc_final: 0.6790 (t0) REVERT: B 105 ASP cc_start: 0.8637 (t0) cc_final: 0.8204 (t0) REVERT: B 116 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.8446 (m-80) REVERT: B 120 ARG cc_start: 0.8582 (mpp80) cc_final: 0.7819 (mmm-85) REVERT: B 242 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8655 (t80) REVERT: B 250 GLU cc_start: 0.8324 (pm20) cc_final: 0.7885 (pm20) REVERT: B 331 TRP cc_start: 0.7876 (t60) cc_final: 0.7518 (t60) REVERT: C 52 ASP cc_start: 0.7703 (t0) cc_final: 0.6930 (t0) REVERT: D 52 ASP cc_start: 0.7401 (t0) cc_final: 0.6910 (t0) REVERT: D 99 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8386 (pp) REVERT: D 120 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8053 (mtp85) REVERT: E 52 ASP cc_start: 0.7518 (t70) cc_final: 0.6964 (t70) REVERT: E 103 PHE cc_start: 0.8604 (m-80) cc_final: 0.8389 (m-10) REVERT: E 108 LYS cc_start: 0.8346 (mtmm) cc_final: 0.7968 (mtmm) REVERT: E 201 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7281 (mm) REVERT: E 221 LEU cc_start: 0.8896 (tp) cc_final: 0.8531 (mm) REVERT: E 328 ARG cc_start: 0.4970 (OUTLIER) cc_final: 0.4457 (mmm-85) outliers start: 42 outliers final: 23 residues processed: 183 average time/residue: 0.5400 time to fit residues: 111.7611 Evaluate side-chains 179 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR 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 B residue 91 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 103 PHE 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 263 SER 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 99 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 227 LEU 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: 5.9990 chunk 79 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 179 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.125943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.100155 restraints weight = 20913.262| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.46 r_work: 0.3003 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 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 = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17140 Z= 0.120 Angle : 0.533 7.266 23475 Z= 0.264 Chirality : 0.042 0.167 2760 Planarity : 0.004 0.042 2820 Dihedral : 4.764 38.177 2792 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.03 % Allowed : 18.13 % 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 aren not related in a simple way. whole: 1.78 (0.19), residues: 1930 helix: 3.46 (0.17), residues: 775 sheet: -1.08 (0.23), residues: 440 loop : 0.17 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 315 TYR 0.016 0.001 TYR B 67 PHE 0.006 0.001 PHE C 233 TRP 0.028 0.001 TRP E 456 HIS 0.002 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00272 (17115) covalent geometry : angle 0.52624 (23400) hydrogen bonds : bond 0.03859 ( 904) hydrogen bonds : angle 4.07044 ( 2742) link_BETA1-4 : bond 0.00309 ( 10) link_BETA1-4 : angle 1.76616 ( 30) link_NAG-ASN : bond 0.00165 ( 15) link_NAG-ASN : angle 1.54422 ( 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 191 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.754 Fit side-chains REVERT: A 17 ASP cc_start: 0.7911 (t0) cc_final: 0.6973 (m-30) REVERT: A 52 ASP cc_start: 0.7534 (t0) cc_final: 0.6655 (t70) REVERT: A 54 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7607 (mtmt) REVERT: A 105 ASP cc_start: 0.8352 (t0) cc_final: 0.7897 (t0) REVERT: A 116 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8464 (m-80) REVERT: A 184 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6081 (pm20) REVERT: A 328 ARG cc_start: 0.4969 (OUTLIER) cc_final: 0.4409 (mmm-85) REVERT: A 421 GLU cc_start: 0.7000 (tt0) cc_final: 0.6767 (mm-30) REVERT: B 52 ASP cc_start: 0.7433 (t0) cc_final: 0.6738 (t0) REVERT: B 105 ASP cc_start: 0.8534 (t0) cc_final: 0.8172 (t0) REVERT: B 116 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.8436 (m-80) REVERT: B 120 ARG cc_start: 0.8543 (mpp80) cc_final: 0.7836 (mmm-85) REVERT: B 331 TRP cc_start: 0.7911 (t60) cc_final: 0.7525 (t60) REVERT: B 434 ASP cc_start: 0.8746 (t0) cc_final: 0.8467 (t0) REVERT: C 52 ASP cc_start: 0.7671 (t0) cc_final: 0.6844 (t0) REVERT: C 434 ASP cc_start: 0.8545 (t0) cc_final: 0.8237 (t0) REVERT: D 17 ASP cc_start: 0.7985 (t0) cc_final: 0.7029 (m-30) REVERT: D 52 ASP cc_start: 0.7403 (t0) cc_final: 0.6883 (t0) REVERT: D 99 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8309 (pp) REVERT: D 120 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8075 (mtp85) REVERT: E 52 ASP cc_start: 0.7548 (t70) cc_final: 0.7001 (t70) REVERT: E 92 SER cc_start: 0.9138 (m) cc_final: 0.8762 (p) REVERT: E 103 PHE cc_start: 0.8625 (m-80) cc_final: 0.8419 (m-10) REVERT: E 108 LYS cc_start: 0.8415 (mtmm) cc_final: 0.8065 (mtmm) REVERT: E 201 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7336 (mm) REVERT: E 221 LEU cc_start: 0.8880 (tp) cc_final: 0.8528 (mm) REVERT: E 328 ARG cc_start: 0.4906 (OUTLIER) cc_final: 0.4531 (mmm-85) outliers start: 37 outliers final: 22 residues processed: 181 average time/residue: 0.5505 time to fit residues: 113.0169 Evaluate side-chains 180 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 116 TYR 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 269 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 103 PHE 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 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 263 SER 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 99 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 227 LEU 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: 0.8980 chunk 18 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 183 optimal weight: 0.0070 chunk 141 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.126097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.100317 restraints weight = 20870.175| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.44 r_work: 0.3008 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 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 = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17140 Z= 0.117 Angle : 0.541 12.703 23475 Z= 0.264 Chirality : 0.042 0.197 2760 Planarity : 0.004 0.042 2820 Dihedral : 4.633 30.720 2792 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.76 % Allowed : 18.41 % 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 aren not related in a simple way. whole: 1.80 (0.19), residues: 1930 helix: 3.47 (0.17), residues: 780 sheet: -1.06 (0.23), residues: 440 loop : 0.17 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 315 TYR 0.016 0.001 TYR B 67 PHE 0.007 0.001 PHE A 233 TRP 0.028 0.001 TRP E 456 HIS 0.002 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00264 (17115) covalent geometry : angle 0.53446 (23400) hydrogen bonds : bond 0.03817 ( 904) hydrogen bonds : angle 4.02236 ( 2742) link_BETA1-4 : bond 0.00278 ( 10) link_BETA1-4 : angle 1.75494 ( 30) link_NAG-ASN : bond 0.00174 ( 15) link_NAG-ASN : angle 1.51040 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4784.19 seconds wall clock time: 82 minutes 41.89 seconds (4961.89 seconds total)