Starting phenix.real_space_refine on Sun May 18 09:03:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cc7_16557/05_2025/8cc7_16557.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cc7_16557/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cc7_16557/05_2025/8cc7_16557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cc7_16557/05_2025/8cc7_16557.map" model { file = "/net/cci-nas-00/data/ceres_data/8cc7_16557/05_2025/8cc7_16557.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cc7_16557/05_2025/8cc7_16557.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.61, per 1000 atoms: 0.64 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: 4.82 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.73 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: 5.71 Time building geometry restraints manager: 5.49 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 460) selection = (chain 'B' and resid 8 through 460) selection = (chain 'C' and resid 8 through 460) selection = (chain 'D' and resid 8 through 460) selection = (chain 'E' and resid 8 through 460) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 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: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 39.760 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.950 ------------------------------------------------------------------------------- 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 : 5.22 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.025 0.001 TRP C 456 HIS 0.002 0.001 HIS C 18 PHE 0.009 0.001 PHE B 181 TYR 0.015 0.001 TYR A 262 ARG 0.010 0.000 ARG D 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00112 ( 15) link_NAG-ASN : angle 1.18001 ( 45) link_BETA1-4 : bond 0.00238 ( 10) link_BETA1-4 : angle 1.88923 ( 30) hydrogen bonds : bond 0.14290 ( 904) hydrogen bonds : angle 6.12211 ( 2742) covalent geometry : bond 0.00403 (17115) covalent geometry : angle 0.64733 (23400) *********************** 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 : 1.766 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: 1.1564 time to fit residues: 231.1967 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 : 1.956 ------------------------------------------------------------------------------- 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 164 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 99 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.124320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.098697 restraints weight = 21270.060| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.47 r_work: 0.2975 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 17140 Z= 0.171 Angle : 0.558 5.546 23475 Z= 0.281 Chirality : 0.044 0.156 2760 Planarity : 0.004 0.040 2820 Dihedral : 6.552 59.635 2804 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.53 % Allowed : 16.65 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.19), residues: 1930 helix: 3.32 (0.17), residues: 775 sheet: -0.83 (0.23), residues: 435 loop : 0.35 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 456 HIS 0.003 0.001 HIS B 411 PHE 0.008 0.001 PHE C 303 TYR 0.018 0.001 TYR B 67 ARG 0.007 0.001 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 15) link_NAG-ASN : angle 1.85686 ( 45) link_BETA1-4 : bond 0.00204 ( 10) link_BETA1-4 : angle 1.61232 ( 30) hydrogen bonds : bond 0.04504 ( 904) hydrogen bonds : angle 4.59669 ( 2742) covalent geometry : bond 0.00411 (17115) covalent geometry : angle 0.55001 (23400) *********************** 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 204 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 2.025 Fit side-chains REVERT: A 52 ASP cc_start: 0.7693 (t0) cc_final: 0.6909 (t0) REVERT: A 54 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7753 (mtmm) REVERT: A 105 ASP cc_start: 0.8243 (t0) cc_final: 0.7924 (t0) REVERT: A 184 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6105 (pm20) REVERT: B 184 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6079 (pm20) REVERT: C 50 ASN cc_start: 0.8185 (t0) cc_final: 0.7913 (t0) REVERT: D 17 ASP cc_start: 0.7271 (m-30) cc_final: 0.7050 (m-30) REVERT: D 120 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7996 (mtp85) REVERT: E 103 PHE cc_start: 0.8563 (m-80) cc_final: 0.8326 (m-10) REVERT: E 311 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7202 (pp30) outliers start: 46 outliers final: 15 residues processed: 189 average time/residue: 1.1829 time to fit residues: 252.0476 Evaluate side-chains 167 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 263 SER 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 263 SER Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 453 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 110 optimal weight: 0.9980 chunk 166 optimal weight: 0.0020 chunk 47 optimal weight: 0.1980 chunk 81 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 HIS 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 = 0.126547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.100494 restraints weight = 20927.066| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.47 r_work: 0.3013 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- 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: 0.7521 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 0.025 17140 Z= 0.106 Angle : 0.497 6.046 23475 Z= 0.251 Chirality : 0.042 0.146 2760 Planarity : 0.004 0.037 2820 Dihedral : 6.014 59.653 2794 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.24 % Allowed : 16.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.19), residues: 1930 helix: 3.49 (0.17), residues: 775 sheet: -0.90 (0.24), residues: 415 loop : 0.30 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 456 HIS 0.002 0.001 HIS B 119 PHE 0.006 0.001 PHE A 233 TYR 0.014 0.001 TYR B 67 ARG 0.006 0.000 ARG B 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00078 ( 15) link_NAG-ASN : angle 1.47537 ( 45) link_BETA1-4 : bond 0.00317 ( 10) link_BETA1-4 : angle 1.67324 ( 30) hydrogen bonds : bond 0.04081 ( 904) hydrogen bonds : angle 4.36259 ( 2742) covalent geometry : bond 0.00225 (17115) covalent geometry : angle 0.48986 (23400) *********************** 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 224 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 165 time to evaluate : 2.056 Fit side-chains REVERT: A 52 ASP cc_start: 0.7513 (t0) cc_final: 0.6765 (t0) REVERT: A 54 LYS cc_start: 0.8256 (mtmm) cc_final: 0.7712 (mtmm) REVERT: A 105 ASP cc_start: 0.8176 (t0) cc_final: 0.7794 (t0) REVERT: B 52 ASP cc_start: 0.7515 (t0) cc_final: 0.6904 (t0) REVERT: B 105 ASP cc_start: 0.8481 (t0) cc_final: 0.8061 (t0) REVERT: B 250 GLU cc_start: 0.7985 (pt0) cc_final: 0.7632 (pm20) REVERT: B 434 ASP cc_start: 0.8616 (t0) cc_final: 0.8390 (t0) REVERT: C 184 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: C 201 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7663 (mm) REVERT: C 328 ARG cc_start: 0.4827 (OUTLIER) cc_final: 0.4395 (mmm-85) REVERT: C 434 ASP cc_start: 0.8412 (t0) cc_final: 0.8158 (t0) REVERT: D 52 ASP cc_start: 0.7265 (t0) cc_final: 0.6798 (t0) REVERT: D 99 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8284 (pp) REVERT: D 105 ASP cc_start: 0.8409 (t0) cc_final: 0.8181 (t0) REVERT: D 120 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7988 (mtp85) REVERT: D 315 ARG cc_start: 0.8440 (mtp85) cc_final: 0.8226 (mmm160) REVERT: E 52 ASP cc_start: 0.7668 (t70) cc_final: 0.6879 (t0) REVERT: E 103 PHE cc_start: 0.8562 (m-80) cc_final: 0.8332 (m-10) REVERT: E 108 LYS cc_start: 0.8444 (mtmm) cc_final: 0.8171 (mtmm) REVERT: E 201 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7540 (mm) REVERT: E 311 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7201 (pp30) REVERT: E 328 ARG cc_start: 0.4978 (OUTLIER) cc_final: 0.4422 (mmm-85) outliers start: 59 outliers final: 16 residues processed: 210 average time/residue: 1.0351 time to fit residues: 247.9608 Evaluate side-chains 180 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 210 MET Chi-restraints excluded: chain B residue 221 LEU 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 184 GLN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 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 91 ASP Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 328 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 101 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 2 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 55 ASN C 183 ASN D 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.101235 restraints weight = 20926.923| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.49 r_work: 0.3009 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 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 = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17140 Z= 0.106 Angle : 0.495 7.284 23475 Z= 0.249 Chirality : 0.042 0.167 2760 Planarity : 0.004 0.040 2820 Dihedral : 5.737 57.460 2794 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.74 % Allowed : 16.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.19), residues: 1930 helix: 3.49 (0.17), residues: 775 sheet: -0.91 (0.24), residues: 415 loop : 0.31 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 456 HIS 0.002 0.001 HIS D 18 PHE 0.005 0.001 PHE C 233 TYR 0.019 0.001 TYR C 64 ARG 0.007 0.000 ARG B 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 15) link_NAG-ASN : angle 1.47333 ( 45) link_BETA1-4 : bond 0.00295 ( 10) link_BETA1-4 : angle 1.65954 ( 30) hydrogen bonds : bond 0.03898 ( 904) hydrogen bonds : angle 4.21616 ( 2742) covalent geometry : bond 0.00230 (17115) covalent geometry : angle 0.48812 (23400) *********************** 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 228 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 160 time to evaluate : 1.937 Fit side-chains REVERT: A 52 ASP cc_start: 0.7529 (t0) cc_final: 0.6691 (t0) REVERT: A 54 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7611 (mtmm) REVERT: A 105 ASP cc_start: 0.8195 (t0) cc_final: 0.7680 (t0) REVERT: B 52 ASP cc_start: 0.7373 (t0) cc_final: 0.6611 (t0) REVERT: B 105 ASP cc_start: 0.8453 (t0) cc_final: 0.7989 (t0) REVERT: B 120 ARG cc_start: 0.8364 (mpp80) cc_final: 0.7746 (mmm-85) REVERT: B 184 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.6051 (pm20) REVERT: B 250 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7858 (pm20) REVERT: B 311 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7391 (pm20) REVERT: B 434 ASP cc_start: 0.8613 (t0) cc_final: 0.8382 (t0) REVERT: C 52 ASP cc_start: 0.7504 (t0) cc_final: 0.6991 (t0) REVERT: C 201 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7773 (mm) REVERT: C 328 ARG cc_start: 0.5090 (OUTLIER) cc_final: 0.4334 (mmm-85) REVERT: C 434 ASP cc_start: 0.8410 (t0) cc_final: 0.8153 (t0) REVERT: D 17 ASP cc_start: 0.7889 (t0) cc_final: 0.6970 (m-30) REVERT: D 52 ASP cc_start: 0.7280 (t0) cc_final: 0.6804 (t0) REVERT: D 105 ASP cc_start: 0.8367 (t0) cc_final: 0.8166 (t0) REVERT: D 120 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7954 (mtp85) REVERT: D 315 ARG cc_start: 0.8487 (mtp85) cc_final: 0.8280 (mmm160) REVERT: E 17 ASP cc_start: 0.7775 (t0) cc_final: 0.6891 (m-30) REVERT: E 52 ASP cc_start: 0.7564 (t70) cc_final: 0.6882 (t0) REVERT: E 103 PHE cc_start: 0.8515 (m-80) cc_final: 0.8292 (m-10) REVERT: E 108 LYS cc_start: 0.8476 (mtmm) cc_final: 0.8058 (mtmm) REVERT: E 201 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7448 (mm) REVERT: E 328 ARG cc_start: 0.4866 (OUTLIER) cc_final: 0.4507 (mmm-85) outliers start: 68 outliers final: 19 residues processed: 211 average time/residue: 1.0413 time to fit residues: 250.2754 Evaluate side-chains 182 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 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 210 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 328 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 124 optimal weight: 0.6980 chunk 125 optimal weight: 0.0970 chunk 15 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 3 optimal weight: 0.0000 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.127905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.101874 restraints weight = 21034.615| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.49 r_work: 0.3028 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- 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: 0.7500 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17140 Z= 0.097 Angle : 0.489 7.502 23475 Z= 0.244 Chirality : 0.042 0.167 2760 Planarity : 0.004 0.040 2820 Dihedral : 5.415 55.614 2794 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.58 % Allowed : 16.76 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.19), residues: 1930 helix: 3.55 (0.17), residues: 775 sheet: -0.79 (0.24), residues: 400 loop : 0.31 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 456 HIS 0.002 0.000 HIS B 119 PHE 0.007 0.001 PHE E 242 TYR 0.013 0.001 TYR D 67 ARG 0.008 0.000 ARG B 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00093 ( 15) link_NAG-ASN : angle 1.41034 ( 45) link_BETA1-4 : bond 0.00338 ( 10) link_BETA1-4 : angle 1.67880 ( 30) hydrogen bonds : bond 0.03723 ( 904) hydrogen bonds : angle 4.11619 ( 2742) covalent geometry : bond 0.00201 (17115) covalent geometry : angle 0.48207 (23400) *********************** 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 206 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 1.817 Fit side-chains REVERT: A 52 ASP cc_start: 0.7487 (t0) cc_final: 0.6639 (t0) REVERT: A 54 LYS cc_start: 0.8188 (mtmm) cc_final: 0.7563 (mtmm) REVERT: A 105 ASP cc_start: 0.8153 (t0) cc_final: 0.7717 (t0) REVERT: A 184 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.6030 (pm20) REVERT: A 328 ARG cc_start: 0.4847 (OUTLIER) cc_final: 0.4567 (mmm-85) REVERT: B 52 ASP cc_start: 0.7403 (t0) cc_final: 0.6685 (t0) REVERT: B 105 ASP cc_start: 0.8426 (t0) cc_final: 0.7957 (t0) REVERT: B 184 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6122 (pm20) REVERT: B 250 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7840 (pm20) REVERT: B 315 ARG cc_start: 0.8358 (mtp85) cc_final: 0.8032 (mmm-85) REVERT: B 328 ARG cc_start: 0.4695 (OUTLIER) cc_final: 0.4022 (mtt-85) REVERT: B 434 ASP cc_start: 0.8574 (t0) cc_final: 0.8330 (t0) REVERT: C 17 ASP cc_start: 0.7837 (t0) cc_final: 0.7220 (m-30) REVERT: C 52 ASP cc_start: 0.7518 (t0) cc_final: 0.6774 (t0) REVERT: C 201 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7648 (mm) REVERT: C 328 ARG cc_start: 0.5074 (OUTLIER) cc_final: 0.4303 (mtt-85) REVERT: C 434 ASP cc_start: 0.8436 (t0) cc_final: 0.8198 (t0) REVERT: D 17 ASP cc_start: 0.7848 (t0) cc_final: 0.7006 (m-30) REVERT: D 52 ASP cc_start: 0.7269 (t0) cc_final: 0.6714 (t0) REVERT: D 120 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7904 (mtp85) REVERT: D 315 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8222 (mmm160) REVERT: E 17 ASP cc_start: 0.7795 (t0) cc_final: 0.6889 (m-30) REVERT: E 52 ASP cc_start: 0.7505 (t70) cc_final: 0.6832 (t0) REVERT: E 103 PHE cc_start: 0.8456 (m-80) cc_final: 0.8212 (m-10) REVERT: E 108 LYS cc_start: 0.8416 (mtmm) cc_final: 0.8094 (mtmm) REVERT: E 201 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7370 (mm) REVERT: E 328 ARG cc_start: 0.4869 (OUTLIER) cc_final: 0.4317 (mmm-85) outliers start: 47 outliers final: 16 residues processed: 196 average time/residue: 1.1140 time to fit residues: 246.5712 Evaluate side-chains 177 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 28 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 173 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.126112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.100171 restraints weight = 21166.385| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.49 r_work: 0.3000 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 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 = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17140 Z= 0.128 Angle : 0.507 6.644 23475 Z= 0.253 Chirality : 0.042 0.170 2760 Planarity : 0.004 0.041 2820 Dihedral : 5.311 48.116 2794 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.69 % Allowed : 16.87 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.19), residues: 1930 helix: 3.45 (0.17), residues: 775 sheet: -0.80 (0.24), residues: 400 loop : 0.25 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 456 HIS 0.002 0.001 HIS D 18 PHE 0.006 0.001 PHE E 233 TYR 0.016 0.001 TYR B 67 ARG 0.008 0.000 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 15) link_NAG-ASN : angle 1.59326 ( 45) link_BETA1-4 : bond 0.00231 ( 10) link_BETA1-4 : angle 1.69635 ( 30) hydrogen bonds : bond 0.03861 ( 904) hydrogen bonds : angle 4.10748 ( 2742) covalent geometry : bond 0.00294 (17115) covalent geometry : angle 0.49885 (23400) *********************** 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 209 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 1.899 Fit side-chains REVERT: A 52 ASP cc_start: 0.7517 (t0) cc_final: 0.6691 (t0) REVERT: A 54 LYS cc_start: 0.8217 (mtmm) cc_final: 0.7680 (mtmm) REVERT: A 79 ASP cc_start: 0.8528 (m-30) cc_final: 0.8283 (m-30) REVERT: A 105 ASP cc_start: 0.8192 (t0) cc_final: 0.7745 (t0) REVERT: A 184 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6128 (pm20) REVERT: B 52 ASP cc_start: 0.7438 (t0) cc_final: 0.6741 (t0) REVERT: B 105 ASP cc_start: 0.8450 (t0) cc_final: 0.8019 (t0) REVERT: B 120 ARG cc_start: 0.8360 (mpp80) cc_final: 0.7843 (mmm-85) REVERT: B 184 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6051 (pm20) REVERT: B 315 ARG cc_start: 0.8461 (mtp85) cc_final: 0.8136 (mmm-85) REVERT: B 434 ASP cc_start: 0.8644 (t0) cc_final: 0.8386 (t0) REVERT: C 52 ASP cc_start: 0.7544 (t0) cc_final: 0.6787 (t0) REVERT: C 201 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7638 (mm) REVERT: D 17 ASP cc_start: 0.7945 (t0) cc_final: 0.7038 (m-30) REVERT: D 52 ASP cc_start: 0.7247 (t0) cc_final: 0.6750 (t0) REVERT: D 120 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7955 (mtp85) REVERT: D 315 ARG cc_start: 0.8465 (mtp85) cc_final: 0.8248 (mmm160) REVERT: E 17 ASP cc_start: 0.7831 (t0) cc_final: 0.7461 (OUTLIER) REVERT: E 52 ASP cc_start: 0.7461 (t70) cc_final: 0.6720 (t0) REVERT: E 103 PHE cc_start: 0.8539 (m-80) cc_final: 0.8304 (m-10) REVERT: E 108 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8108 (mtmm) REVERT: E 201 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7312 (mm) REVERT: E 221 LEU cc_start: 0.8877 (tp) cc_final: 0.8529 (mm) REVERT: E 328 ARG cc_start: 0.4911 (OUTLIER) cc_final: 0.4348 (mmm-85) outliers start: 49 outliers final: 26 residues processed: 197 average time/residue: 1.0252 time to fit residues: 230.5976 Evaluate side-chains 185 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 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 269 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 140 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.126692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.100769 restraints weight = 20964.118| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.48 r_work: 0.3005 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 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 = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17140 Z= 0.116 Angle : 0.503 6.468 23475 Z= 0.250 Chirality : 0.042 0.166 2760 Planarity : 0.004 0.040 2820 Dihedral : 5.001 41.597 2792 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.69 % Allowed : 16.87 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.19), residues: 1930 helix: 3.50 (0.17), residues: 775 sheet: -0.80 (0.24), residues: 400 loop : 0.21 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 456 HIS 0.002 0.001 HIS B 119 PHE 0.006 0.001 PHE E 233 TYR 0.014 0.001 TYR B 67 ARG 0.008 0.000 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 15) link_NAG-ASN : angle 1.50786 ( 45) link_BETA1-4 : bond 0.00298 ( 10) link_BETA1-4 : angle 1.70639 ( 30) hydrogen bonds : bond 0.03786 ( 904) hydrogen bonds : angle 4.05872 ( 2742) covalent geometry : bond 0.00259 (17115) covalent geometry : angle 0.49612 (23400) *********************** 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: 49 poor density : 156 time to evaluate : 1.750 Fit side-chains REVERT: A 52 ASP cc_start: 0.7462 (t0) cc_final: 0.6549 (t0) REVERT: A 54 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7603 (mtmt) REVERT: A 79 ASP cc_start: 0.8504 (m-30) cc_final: 0.8249 (m-30) REVERT: A 105 ASP cc_start: 0.8179 (t0) cc_final: 0.7730 (t0) REVERT: A 184 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6014 (pm20) REVERT: B 52 ASP cc_start: 0.7367 (t0) cc_final: 0.6712 (t0) REVERT: B 105 ASP cc_start: 0.8446 (t0) cc_final: 0.8048 (t0) REVERT: B 120 ARG cc_start: 0.8353 (mpp80) cc_final: 0.7802 (mmm-85) REVERT: B 184 GLN cc_start: 0.6941 (OUTLIER) cc_final: 0.6006 (pm20) REVERT: B 242 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8554 (t80) REVERT: B 250 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7656 (pm20) REVERT: B 315 ARG cc_start: 0.8494 (mtp85) cc_final: 0.8151 (mmm-85) REVERT: B 434 ASP cc_start: 0.8630 (t0) cc_final: 0.8370 (t0) REVERT: C 52 ASP cc_start: 0.7524 (t0) cc_final: 0.6718 (t0) REVERT: C 201 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7579 (mm) REVERT: D 17 ASP cc_start: 0.7903 (t0) cc_final: 0.7051 (m-30) REVERT: D 52 ASP cc_start: 0.7291 (t0) cc_final: 0.6738 (t0) REVERT: D 120 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7909 (mtp85) REVERT: D 315 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8221 (mmm160) REVERT: E 17 ASP cc_start: 0.7830 (t0) cc_final: 0.7469 (OUTLIER) REVERT: E 52 ASP cc_start: 0.7412 (t70) cc_final: 0.6786 (t70) REVERT: E 103 PHE cc_start: 0.8519 (m-80) cc_final: 0.8282 (m-10) REVERT: E 108 LYS cc_start: 0.8369 (mtmm) cc_final: 0.8059 (mtmm) REVERT: E 201 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7367 (mm) REVERT: E 221 LEU cc_start: 0.8887 (tp) cc_final: 0.8539 (mm) REVERT: E 328 ARG cc_start: 0.4897 (OUTLIER) cc_final: 0.4344 (mmm-85) outliers start: 49 outliers final: 28 residues processed: 193 average time/residue: 1.0209 time to fit residues: 224.7134 Evaluate side-chains 184 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 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 242 PHE Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 332 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 182 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.124661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.098764 restraints weight = 21140.934| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.47 r_work: 0.2979 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 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 = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17140 Z= 0.163 Angle : 0.544 7.712 23475 Z= 0.269 Chirality : 0.043 0.170 2760 Planarity : 0.004 0.044 2820 Dihedral : 5.046 37.266 2792 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.31 % Allowed : 17.75 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.19), residues: 1930 helix: 3.37 (0.17), residues: 775 sheet: -1.08 (0.23), residues: 440 loop : 0.19 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 456 HIS 0.003 0.001 HIS A 18 PHE 0.007 0.001 PHE C 303 TYR 0.022 0.001 TYR B 67 ARG 0.009 0.000 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 15) link_NAG-ASN : angle 1.74157 ( 45) link_BETA1-4 : bond 0.00207 ( 10) link_BETA1-4 : angle 1.78670 ( 30) hydrogen bonds : bond 0.04026 ( 904) hydrogen bonds : angle 4.12395 ( 2742) covalent geometry : bond 0.00390 (17115) covalent geometry : angle 0.53576 (23400) *********************** 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 195 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 1.983 Fit side-chains REVERT: A 17 ASP cc_start: 0.7966 (t0) cc_final: 0.7017 (m-30) REVERT: A 52 ASP cc_start: 0.7575 (t0) cc_final: 0.6671 (t70) REVERT: A 54 LYS cc_start: 0.8200 (mtmm) cc_final: 0.7701 (mtmt) REVERT: A 79 ASP cc_start: 0.8575 (m-30) cc_final: 0.8355 (m-30) REVERT: A 105 ASP cc_start: 0.8369 (t0) cc_final: 0.7903 (t0) REVERT: A 184 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6052 (pm20) REVERT: B 52 ASP cc_start: 0.7463 (t0) cc_final: 0.6794 (t0) REVERT: B 105 ASP cc_start: 0.8622 (t0) cc_final: 0.8251 (t0) REVERT: B 116 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.8490 (m-80) REVERT: B 120 ARG cc_start: 0.8521 (mpp80) cc_final: 0.7860 (mmm-85) REVERT: B 184 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6046 (pm20) REVERT: B 250 GLU cc_start: 0.8298 (pm20) cc_final: 0.7793 (pm20) REVERT: B 434 ASP cc_start: 0.8778 (t0) cc_final: 0.8574 (t0) REVERT: C 52 ASP cc_start: 0.7646 (t0) cc_final: 0.6929 (t0) REVERT: C 184 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7026 (tm-30) REVERT: C 201 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7647 (mm) REVERT: D 52 ASP cc_start: 0.7426 (t0) cc_final: 0.6920 (t0) REVERT: D 120 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8095 (mtp85) REVERT: E 17 ASP cc_start: 0.8003 (t0) cc_final: 0.7797 (t0) REVERT: E 52 ASP cc_start: 0.7515 (t70) cc_final: 0.6899 (t70) REVERT: E 103 PHE cc_start: 0.8661 (m-80) cc_final: 0.8450 (m-10) REVERT: E 108 LYS cc_start: 0.8343 (mtmm) cc_final: 0.8010 (mtmm) REVERT: E 201 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7369 (mm) REVERT: E 221 LEU cc_start: 0.8910 (tp) cc_final: 0.8565 (mm) REVERT: E 328 ARG cc_start: 0.4969 (OUTLIER) cc_final: 0.4547 (mmm-85) outliers start: 42 outliers final: 26 residues processed: 188 average time/residue: 1.0364 time to fit residues: 221.9691 Evaluate side-chains 177 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 1.747 ------------------------------------------------------------------------------- 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 A residue 332 ILE 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 269 VAL Chi-restraints excluded: chain C residue 201 ILE 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 269 VAL Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 159 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 175 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.124189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.098317 restraints weight = 21127.010| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.46 r_work: 0.2974 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 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 = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17140 Z= 0.175 Angle : 0.558 6.861 23475 Z= 0.276 Chirality : 0.044 0.170 2760 Planarity : 0.004 0.043 2820 Dihedral : 5.074 33.247 2792 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.58 % Allowed : 17.75 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.19), residues: 1930 helix: 3.32 (0.17), residues: 775 sheet: -1.03 (0.23), residues: 430 loop : 0.11 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 456 HIS 0.003 0.001 HIS B 411 PHE 0.008 0.001 PHE A 233 TYR 0.021 0.001 TYR B 67 ARG 0.009 0.000 ARG B 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 15) link_NAG-ASN : angle 1.78530 ( 45) link_BETA1-4 : bond 0.00223 ( 10) link_BETA1-4 : angle 1.83463 ( 30) hydrogen bonds : bond 0.04119 ( 904) hydrogen bonds : angle 4.16370 ( 2742) covalent geometry : bond 0.00421 (17115) covalent geometry : angle 0.54943 (23400) *********************** 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 192 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 145 time to evaluate : 2.023 Fit side-chains REVERT: A 52 ASP cc_start: 0.7587 (t0) cc_final: 0.6679 (t70) REVERT: A 54 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7695 (mtmt) REVERT: A 79 ASP cc_start: 0.8580 (m-30) cc_final: 0.8355 (m-30) REVERT: A 105 ASP cc_start: 0.8328 (t0) cc_final: 0.7883 (t0) REVERT: A 116 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8475 (m-80) REVERT: A 184 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6128 (pm20) REVERT: B 52 ASP cc_start: 0.7410 (t0) cc_final: 0.6709 (t0) REVERT: B 105 ASP cc_start: 0.8647 (t0) cc_final: 0.8278 (t0) REVERT: B 116 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8488 (m-80) REVERT: B 120 ARG cc_start: 0.8545 (mpp80) cc_final: 0.7869 (mmm-85) REVERT: B 250 GLU cc_start: 0.8144 (pm20) cc_final: 0.7661 (pm20) REVERT: B 331 TRP cc_start: 0.7878 (t60) cc_final: 0.7530 (t60) REVERT: C 52 ASP cc_start: 0.7692 (t0) cc_final: 0.6978 (t0) REVERT: C 201 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7659 (mm) REVERT: C 235 MET cc_start: 0.7213 (tpp) cc_final: 0.7011 (mmm) REVERT: D 17 ASP cc_start: 0.8036 (t0) cc_final: 0.7172 (m-30) REVERT: D 52 ASP cc_start: 0.7446 (t0) cc_final: 0.6933 (t0) REVERT: D 120 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8064 (mtp85) REVERT: E 17 ASP cc_start: 0.8073 (t0) cc_final: 0.7867 (t0) REVERT: E 52 ASP cc_start: 0.7509 (t70) cc_final: 0.6883 (t70) REVERT: E 108 LYS cc_start: 0.8437 (mtmm) cc_final: 0.8076 (mtmm) REVERT: E 201 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7329 (mm) REVERT: E 328 ARG cc_start: 0.5005 (OUTLIER) cc_final: 0.4384 (mmm-85) REVERT: E 332 ILE cc_start: 0.7353 (mt) cc_final: 0.7115 (mp) outliers start: 47 outliers final: 25 residues processed: 186 average time/residue: 1.0846 time to fit residues: 231.3258 Evaluate side-chains 174 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 1.831 ------------------------------------------------------------------------------- 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 332 ILE 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 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 27 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 193 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.125746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.099964 restraints weight = 21090.904| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.47 r_work: 0.2999 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 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 = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1576 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= 0.122 Angle : 0.528 7.091 23475 Z= 0.262 Chirality : 0.042 0.163 2760 Planarity : 0.004 0.042 2820 Dihedral : 4.829 26.274 2792 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.92 % Allowed : 18.13 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 1930 helix: 3.46 (0.17), residues: 780 sheet: -1.03 (0.23), residues: 430 loop : 0.17 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 456 HIS 0.002 0.001 HIS B 18 PHE 0.007 0.001 PHE C 242 TYR 0.017 0.001 TYR B 67 ARG 0.009 0.000 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 15) link_NAG-ASN : angle 1.56482 ( 45) link_BETA1-4 : bond 0.00286 ( 10) link_BETA1-4 : angle 1.76447 ( 30) hydrogen bonds : bond 0.03881 ( 904) hydrogen bonds : angle 4.06309 ( 2742) covalent geometry : bond 0.00275 (17115) covalent geometry : angle 0.52062 (23400) ********************** 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 186 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 2.003 Fit side-chains REVERT: A 17 ASP cc_start: 0.7935 (t0) cc_final: 0.6995 (m-30) REVERT: A 52 ASP cc_start: 0.7534 (t0) cc_final: 0.6626 (t70) REVERT: A 54 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7641 (mtmt) REVERT: A 105 ASP cc_start: 0.8343 (t0) cc_final: 0.7875 (t0) REVERT: A 116 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.8467 (m-80) REVERT: A 184 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6050 (pm20) REVERT: A 421 GLU cc_start: 0.7009 (tt0) cc_final: 0.6777 (mm-30) REVERT: B 52 ASP cc_start: 0.7410 (t0) cc_final: 0.6710 (t0) REVERT: B 105 ASP cc_start: 0.8608 (t0) cc_final: 0.8201 (t0) REVERT: B 116 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.8464 (m-80) REVERT: B 120 ARG cc_start: 0.8523 (mpp80) cc_final: 0.7845 (mmm-85) REVERT: B 250 GLU cc_start: 0.8283 (pm20) cc_final: 0.7786 (pm20) REVERT: B 331 TRP cc_start: 0.7881 (t60) cc_final: 0.7468 (t60) REVERT: B 418 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6787 (mt-10) REVERT: B 434 ASP cc_start: 0.8749 (t0) cc_final: 0.8452 (t0) REVERT: C 52 ASP cc_start: 0.7652 (t0) cc_final: 0.6915 (t0) REVERT: C 201 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7617 (mm) REVERT: C 328 ARG cc_start: 0.5006 (OUTLIER) cc_final: 0.4280 (mmm-85) REVERT: D 17 ASP cc_start: 0.8018 (t0) cc_final: 0.7153 (m-30) REVERT: D 52 ASP cc_start: 0.7397 (t0) cc_final: 0.6873 (t0) REVERT: D 120 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8070 (mtp85) REVERT: E 52 ASP cc_start: 0.7467 (t70) cc_final: 0.6836 (t70) REVERT: E 92 SER cc_start: 0.9153 (m) cc_final: 0.8756 (p) REVERT: E 108 LYS cc_start: 0.8414 (mtmm) cc_final: 0.8065 (mtmm) REVERT: E 201 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7358 (mm) REVERT: E 221 LEU cc_start: 0.8654 (tp) cc_final: 0.8432 (mm) REVERT: E 328 ARG cc_start: 0.4956 (OUTLIER) cc_final: 0.4349 (mmm-85) outliers start: 35 outliers final: 19 residues processed: 180 average time/residue: 1.0500 time to fit residues: 215.6585 Evaluate side-chains 177 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.816 ------------------------------------------------------------------------------- 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 332 ILE 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 B residue 418 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 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 120 ARG 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 269 VAL 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 75 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.125289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.099305 restraints weight = 21165.785| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.48 r_work: 0.2992 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17140 Z= 0.130 Angle : 0.538 9.222 23475 Z= 0.266 Chirality : 0.043 0.193 2760 Planarity : 0.004 0.043 2820 Dihedral : 4.744 21.290 2792 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.92 % Allowed : 18.46 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.19), residues: 1930 helix: 3.43 (0.17), residues: 780 sheet: -1.09 (0.22), residues: 465 loop : 0.15 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 456 HIS 0.002 0.001 HIS D 18 PHE 0.007 0.001 PHE C 242 TYR 0.017 0.001 TYR B 67 ARG 0.009 0.000 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 15) link_NAG-ASN : angle 1.58808 ( 45) link_BETA1-4 : bond 0.00260 ( 10) link_BETA1-4 : angle 1.75707 ( 30) hydrogen bonds : bond 0.03889 ( 904) hydrogen bonds : angle 4.03909 ( 2742) covalent geometry : bond 0.00300 (17115) covalent geometry : angle 0.53059 (23400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8653.77 seconds wall clock time: 150 minutes 24.70 seconds (9024.70 seconds total)